A fish is not a mouse: understanding differences in background genetics is critical for reproducibility

Looks like home: numerosity, but not spatial frequency guides preference in zebrafish larvae (Danio rerio)

Despite their young age, zebrafish larvae have a well-developed visual system and can distinguish between different visual stimuli. First, we investigated if the first visual surroundings the larvae experience during the first days after hatching shape their habitat preference. Indeed, these animals seem to "imprint" on the first surroundings they see and select visual stimuli accordingly at 7 days post fertilization (dpf). In particular, if zebrafish larvae experience a bar background just after hatching, they later on prefer bars over white stimuli, and vice versa. We then used this acquired preference for bars to investigate innate numerical abilities. We wanted to specifically test if the zebrafish larvae show real numerical abilities or if they rely on a lower-level mechanism-i.e. spatial frequency-to discriminate between two different numerosities. When we matched the spatial frequency in stimuli with different numbers of bars, the larvae reliably selected the higher numerosity. A previous study has ruled out that 7 dpf zebrafish larvae use convex hull, cumulative surface area and density to choose between two numerosities. Therefore, our results indicate that zebrafish larvae rely on real numerical abilities rather than other cues, including spatial frequency, when spontaneously comparing two sets with different numbers of bars.

A practical guide for the husbandry of cave and surface invertebrates as the first step in establishing new model organisms

While extensive research on traditional model species has significantly advanced the biological sciences, the ongoing search for new model organisms is essential to tackle contemporary challenges such as human diseases or climate change, and fundamental phenomena including adaptation or speciation. Recent methodological advances such as next-generation sequencing, gene editing, and imaging are widely applicable and have simplified the selection of species with specific traits from the wild. However, a critical milestone in this endeavor remains the successful cultivation of selected species. A historically overlooked but increasingly recognized group of non-model organisms are cave dwellers. These unique animals offer invaluable insights into the genetic basis of human diseases like eye degeneration, metabolic and neurological disorders, and basic evolutionary principles and the origin of adaptive phenotypes. However, to take advantage of the beneficial traits of cave-dwelling animals, laboratory cultures must be established-a practice that remains extremely rare except for the cavefish Astyanax mexicanus. For most cave-dwelling organisms, there are no published culturing protocols. In this study, we present the results of our multi-year effort to establish laboratory cultures for a variety of invertebrate groups. We have developed comprehensive protocols for housing, feeding, and husbandry of cave dwellers and their surface relatives. Our recommendations are versatile and can be applied to a wide range of species. Hopefully our efforts will facilitate the establishment of new laboratory animal facilities for cave-dwelling organisms and encourage their greater use in experimental biology.

Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models

Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.

Standardization of zebrafish drug testing parameters for muscle diseases

Skeletal muscular diseases predominantly affect skeletal and cardiac muscle, resulting in muscle weakness, impaired respiratory function and decreased lifespan. These harmful outcomes lead to poor health-related quality of life and carry a high healthcare economic burden. The absence of promising treatments and new therapies for muscular disorders requires new methods for candidate drug identification and advancement in animal models. Consequently, the rapid screening of drug compounds in an animal model that mimics features of human muscle disease is warranted. Zebrafish are a versatile model in preclinical studies that support developmental biology and drug discovery programs for novel chemical entities and repurposing of established drugs. Due to several advantages, there is an increasing number of applications of the zebrafish model for high-throughput drug screening for human disorders and developmental studies. Consequently, standardization of key drug screening parameters, such as animal husbandry protocols, drug compound administration and outcome measures, is paramount for the continued advancement of the model and field. Here, we seek to summarize and explore critical drug treatment and drug screening parameters in the zebrafish-based modeling of human muscle diseases. Through improved standardization and harmonization of drug screening parameters and protocols, we aim to promote more effective drug discovery programs.

Assessing Drug Administration Techniques in Zebrafish Models of Neurological Disease

Neurological diseases, including neurodegenerative and neurodevelopmental disorders, affect nearly one in six of the world's population. The burden of the resulting deaths and disability is set to rise during the next few decades as a consequence of an aging population. To address this, zebrafish have become increasingly prominent as a model for studying human neurological diseases and exploring potential therapies. Zebrafish offer numerous benefits, such as genetic homology and brain similarities, complementing traditional mammalian models and serving as a valuable tool for genetic screening and drug discovery. In this comprehensive review, we highlight various drug delivery techniques and systems employed for therapeutic interventions of neurological diseases in zebrafish, and evaluate their suitability. We also discuss the challenges encountered during this process and present potential advancements in innovative techniques.

Shigella induces epigenetic reprogramming of zebrafish neutrophils

Trained immunity is a long-term memory of innate immune cells, generating an improved response upon reinfection. Shigella is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae, we demonstrate that after Shigella training, neutrophils are more efficient at bacterial clearance. We observe that Shigella-induced protection is nonspecific and has differences with training by BCG and β-glucan. Analysis of histone ChIP-seq on trained neutrophils revealed that Shigella training deposits the active H3K4me3 mark on promoter regions of 1612 genes, dramatically changing the epigenetic landscape of neutrophils toward enhanced microbial recognition and mitochondrial ROS production. Last, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.

Evaluation of Media Conductivity and a Combination of Iodine and Sodium Hypochlorite Surface Disinfection on Zebrafish (Danio rerio) Embryo Viability and Morphology

Embryo surface disinfection in either an iodine or sodium hypochlorite (NaOCl) solution is commonly performed on imported zebrafish embryos to decrease pathogen introduction into a facility. The impact of the consecutive use of these disinfectants and the conductivity of the culture media on embryo survival and development post-disinfection have not been evaluated. Iodine (12.5-25 ppm) is effective at eliminating several Mycobacterium species, whereas NaOCl (50-100 ppm) reduces the number of viable Pseudoloma neurophilia spores. Casper and T5D (tropical 5D wild type) embryos reared in media of differing conductivities (0-10, 100-200, 750-950, and 1500-2000 μS) with and without exposure to NaOCl 100 ppm at 6 h post-fertilization were evaluated for survival, hatching success, and morphological defects at 5 days post-fertilization. Additionally, the consecutive use of iodine (12.5 ppm for 2 min) followed by NaOCl (75 or 100 ppm for 10 min), as well as the inverse, was evaluated. Embryo survival was not impacted by embryo rearing media alone; however, survival significantly decreased when embryos were disinfected with 100 ppm NaOCl in media with a conductivity >750-950 μS. Iodine (12 ppm) and NaOCl (75 ppm) used sequentially resulted in >50% survival, whereas the use of 100 ppm NaOCl resulted in high levels of embryo mortality.

Zebrafish Models of Cardiac Disease: From Fortuitous Mutants to Precision Medicine

Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.

The phylogenetic position of zebrafish (Danio rerio) from south african pet shops

BACKGROUND

Zebrafish (Danio rerio), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally.

METHODS AND RESULTS

Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species (Danio kyathit). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the lines from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish.

CONCLUSION

These results can be used to guide the future development of laboratory lines suited to the needs at the UFS.

A Multi-Site Assessment of Anesthetic Overdose, Hypothermic Shock, and Electrical Stunning as Methods of Euthanasia for Zebrafish (Danio rerio) Embryos and Larvae

Euthanasia in zebrafish (Danio rerio) younger than 5 days post fertilization (dpf) is poorly described in the literature, and standardized protocols are lacking, most likely because larvae not capable of independent feeding are often not protected under national legislations. We assessed the euthanasia efficacy in laboratories in different countries of a one hour anesthetic overdose immersion with buffered lidocaine hydrochloride (1 g/L, with or without 50 mL/L of ethanol), buffered tricaine (1 g/L), clove oil (0.1%), benzocaine (1 g/L), or 2-phenoxyethanol (3 mL/L), as well as the efficacy of hypothermic shock (one hour immersion) and electrical stunning (for one minute), on zebrafish at <12 h post fertilization (hpf), 24 hpf, and 4 dpf. Based on the survival/recovery rates 24 h after treatment, the most effective methods were clove oil, lidocaine with ethanol, and electrical stunning. For 4 dpf larvae, signs of aversion during treatment demonstrated that all anesthetics, except lidocaine, induced aversive behavior. Therefore, the most suited euthanasic treatment was lidocaine hydrochloride 1 g/L, buffered with 2 g/L of sodium bicarbonate and mixed with 50 mL/L of ethanol, which euthanized both embryos and larvae in an efficient and stress-free manner. Electrical stunning also euthanized embryos and larvae efficiently and without signs of aversion; this method needs further assessment in other laboratories to draw firm conclusions.

Translational relevance of forward genetic screens in animal models for the study of psychiatric disease

Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.

Behavioral genetics of alcohol's effects in three zebrafish (Danio rerio) populations

Alcohol abuse is one of the most dangerous and serious problems for patients and society. Interpopulation studies are important in understanding how genetic background contributes to the effects of alcohol. In this study, we applied a chronic alcohol exposure protocol in three zebrafish populations (Danio rerio; both sexes; AB, TU, and outbred fish - OB). We analyzed the behavioral responses and mRNA expression involved in neurotransmitter metabolism - th1, tph1, ache, ada1, gaba1, gad1b, and bdnf. Locomotion patterns were similar between populations (increased speed after acute alcohol and unaltered locomotion after chronic and withdrawal treatments). All populations exhibited increased expression of genes associated with locomotion (th1, gad1b, and gaba1) after acute alcohol exposure. Anxiety-like responses increased in AB and TU fish during withdrawal and decreased in AB fish after acute alcohol exposure. Genes related to anxiety-like behavior (tph1 and ada1) were overexpressed in AB and TU fish after acute and withdrawal treatments, while OB fish exhibited unaltered responses. Bdnf levels decreased during withdrawal in AB and OB fish, while TU showed upregulated levels in both chronic and withdrawal treatments. Our results suggest that zebrafish populations respond differently to alcohol exposure, which may contribute to understanding the mechanisms underlying alcohol use and dependence. Moreover, we found that a more diverse genetic background (OB) was related to higher variability in behavioral and mRNA expression, demonstrating that inbred populations (AB and TU) may be useful tools in identifying alcohol use and abuse mechanisms.

Differences in susceptibility to Mycobacterium chelonae in zebrafish (Danio rerio) lines commonly used in scientific research

Mycobacteriosis is one of the most common diseases encountered in laboratory zebrafish. These infections can present a problem to researchers using zebrafish because they may introduce unknown experimental variables. Whilst differences in severity of infections between species of Mycobacterium infecting zebrafish have been well documented, little is known about differences in susceptibility between zebrafish lines. Previous surveys have found higher prevalence in the TU zebrafish line relative to other lines, suggesting that there may be underlying genetic differences in susceptibility. This study investigates Mycobacterium chelonae H1E2-GFP infections in four different zebrafish lines commonly used in research (AB, 5D, casper and TU). Fish were exposed to a labelled (green-fluorescent protein (GFP)) strain of M. chelonae by intraperitoneal injection, and infection status was evaluated after 10 weeks. Visualization of GFP in euthanized fish and histology were used as endpoints. In GFP images, severity was assessed by image analysis, and in histological sections, counts of granulomas containing acid-fast bacteria were used. Results indicated differences in severity of infections between lines, but no significant differences in prevalence.

Laboratory Codes in Nomenclature and Scientific Communication (Advancing Organism Nomenclature in Scientific Communication to Improve Research Reporting and Reproducibility)

Laboratory registration codes, also known as laboratory codes or lab codes, are a key element in standardized laboratory animal and genetic nomenclature. As such they are critical to accurate scientific communication and to research reproducibility and integrity. The original committee on Mouse Genetic Nomenclature published nomenclature conventions for mice genetics in 1940, and then conventions for inbred strains in 1952. Unique designations were needed, and have been in use since the 1950s, for the sources of animals and substrains, for the laboratories that identified new alleles or mutations, and then for developers of transgenes and induced mutations. Current laboratory codes are typically a 2- to 4-letter acronym for an institution or an investigator. Unique codes are assigned from the International Laboratory Code Registry, which was developed and is maintained by ILAR in the National Academies (National Academies of Sciences Engineering and Medicine and previously National Academy of Sciences). As a resource for the global research community, the registry has been online since 1997. Since 2003 mouse and rat genetic and strain nomenclature rules have been reviewed and updated annually as a joint effort of the International Committee on Standardized Genetic Nomenclature for Mice and the Rat Genome and Nomenclature Committee. The current nomenclature conventions (particularly conventions for non-inbred animals) are applicable beyond rodents, although not widely adopted. Ongoing recognition, since at least the 1930s, of the research relevance of genetic backgrounds and origins of animals, and of spontaneous and induced genetic variants speaks to the need for broader application of standardized nomenclature for animals in research, particularly given the increasing numbers and complexities of genetically modified swine, nonhuman primates, fish, and other species.

Specific Pathogen Free - A review of strategies in agriculture, aquaculture, and laboratory mammals and how they inform new recommendations for laboratory zebrafish

Specific pathogen-free (SPF) animals are bred and managed to exclude pathogens associated with significant morbidity or mortality that may secondarily pose a risk to public health, food safety and food security, and research replicability. Generating and maintaining SPF animals requires detailed biosecurity planning for control of housing, environmental, and husbandry factors and a history of regimented pathogen testing. Successful programs involve comprehensive risk analysis and exclusion protocols that are rooted in a thorough understanding of pathogen lifecycle and modes of transmission. In this manuscript we review the current state of SPF in domestic agriculture (pigs and poultry), aquaculture (salmonids and shrimp), and small laboratory mammals. As the use of laboratory fish, especially zebrafish (Danio rerio), as models of human disease is expanding exponentially, it is prudent to define standards for SPF in this field. We use the guiding principles from other SPF industries and evaluate zebrafish pathogens against criteria to be on an SPF list, to propose recommendations for establishing and maintaining SPF laboratory zebrafish.

Molecular and culture-based assessment of the microbiome in a zebrafish (Danio rerio) housing system during set-up and equilibration

BACKGROUND

Zebrafish used in research settings are often housed in recirculating aquaculture systems (RAS) which rely on the system microbiome, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. Commercial RAS must be allowed to equilibrate following installation, before fish can be introduced. There is little information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium in RAS in general.

METHODS

A zebrafish housing system was monitored at multiple different system sites including tank water in six different tanks, pre- and post-particulate filter water, the fluidized bed biofilter substrate, post-carbon filter water, and water leaving the ultra-violet (UV) disinfection unit and entering the tanks. All of these samples were collected in quadruplicate, from prior to population of the system with zebrafish through 18 weeks post-population, and analyzed using both 16S rRNA amplicon sequencing and culture using multiple agars and annotation of isolates via matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry. Sequencing data were analyzed using traditional methods, network analyses of longitudinal data, and integration of culture and sequence data.

RESULTS

The water microbiome, dominated by Cutibacterium and Staphylococcus spp., reached a relatively stable richness and composition by approximately three to four weeks post-population, but continued to evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter and water leaving the UV disinfection unit were distinct from water at all other sites. Core taxa detected using molecular methods comprised 36 amplicon sequence variants, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, and showed moderate agreement with sequencing data.

CONCLUSIONS

The microbiome of commercial RAS used for research zebrafish reaches a relatively stable state by four weeks post-population and would be expected to be suitable for experimental use following that time-point.

The Lymphatic System in Zebrafish Heart Development, Regeneration and Disease Modeling

Heart disease remains the single largest cause of death in developed countries, and novel therapeutic interventions are desperately needed to alleviate this growing burden. The cardiac lymphatic system is the long-overlooked counterpart of the coronary blood vasculature, but its important roles in homeostasis and disease are becoming increasingly apparent. Recently, the cardiac lymphatic vasculature in zebrafish has been described and its role in supporting the potent regenerative response of zebrafish heart tissue investigated. In this review, we discuss these findings in the wider context of lymphatic development, evolution and the promise of this system to open new therapeutic avenues to treat myocardial infarction and other cardiopathologies.