Laboratory fish in biomedical research : biology, husbandry and research applications for zebrafish, medaka, killifish, swordtail fish, cavefish, stickleback, goldfish and danionella translucida

Fish, and particularly zebrafish, have become the fastest-growing segment of the research population. They offer several advantages, in terms of biology and technologies to apply, and thus are employed in numerous research fields. Laboratory Fish in Biomedical Research: Biology, Husbandry and Research Applications for Zebrafish, Medaka, Killifish, Swordtail Fish, Cavefish, Stickleback, Goldfish and Danionella Translucida addresses the relevant and increasing need to collect cutting-edge knowledge on husbandry, maintenance, welfare and experimental protocols of the most common freshwater species under standard laboratory conditions. Provides husbandry and management protocols, devices and water systems Shows strength and weakness of breeding Explores potential scientific applications and experimental protocols. with regards to the most used freshwater fish used for scientific purposes Laboratory Fish in Biomedical Research Copyright Contributors Fish as model systems References 1. Biology and research applications The biology of the zebrafish Geographic distribution Zebrafish appearance and life span Zebrafish phylogeny and genetics Zebrafish embryonic development The history of the zebrafish as laboratory model Resources for the zebrafish model The zebrafish as a model for development and pathology The zebrafish as model in developmental biology The zebrafish as model in pathology The zebrafish as a model for cancer research Transgenic cancer models Engraftment cancer models The zebrafish embryo in drug discovery and high-throughput screens Robotics and tools for automated screening Relevance and limitation of the zebrafish embryo for chemical screening The zebrafish as a model for toxicology The zebrafish as model for neurodegenerative diseases Alzheimer's disease Amyotrophic lateral sclerosis Lessons from the zebrafish model on muscle dystrophies References 2. Housing and maintenance of zebrafish, new technologies in laboratory aquatic systems and considerations for facility design Introduction to the model Defining your needs from an animal model and the impact on facility design Primary housing Tank hygiene Aquatic concepts Mechanical filtration Chemical filtration Water disinfection and biological control Biological filtration Establishing biofiltration Denitrification Husbandry Water parameter targets and dealing with anomalies pH Troubleshooting low pH values Troubleshooting high pH values Temperature Temperature troubleshooting Total hardness Carbonate Hardness (KH) General hardness Conductivity/salinity Dissolved gases Dissolved oxygen Carbon dioxide Gas supersaturation Nitrogenous wastes Nitrite Nitrate Nitrogenous waste troubleshooting Chlorine Lighting Feeding Live foods Feeding frequency Maintenance programs Continuity planning Human Mechanical and infrastructure Spare parts New and emerging technologies Acknowledgments References Further reading 3. Breeding and larviculture of zebrafish (Danio rerio) Introduction Should we mimic nature, or should we ignore it in laboratory breeding and husbandry of zebrafish: theoretical consideration ... Zebrafish in nature Preparing zebrafish for breeding The breeding tank Raising zebrafish juveniles is not as easy as often stated Hatching the eggs and caring for the larvae Caring for young juveniles Standardization of breeding and larviculture practices: the question of replicability and reproducibility References 4. Health monitoring, disease, and clinical pathology Introduction Controlling and monitoring population health Husbandry, environmental conditions, and infection pressure Monitoring performance Daily recording of morbidity and mortality Pathogens and diseases to monitor Mycobacterium spp. Pseudocapillaria tomentosa Pseudoloma neurophilia Noninfectious diseases Fish and environmental samples Colony fish Sentinels Environmental samples Diagnostic assays Necropsy and fresh mounts Histopathology Polymerase chain reaction Determining the number of samples Defining an epidemiological unit Specific pathogen free for a threshold prevalence Number of fish sample Introduction of zebrafish colonies and biosecurity Triage of imports Quarantine Biosecurity Conclusion Acknowledgments References 5. The welfare of zebrafish Introduction Measuring welfare in zebrafish Behavioral stress response Neuroendocrine stress response Husbandry Environmental enrichment Strains, genetic modifications, and harmful phenotypes Refinements in regulated procedures Pain and analgesic considerations Anaesthetic aversiveness Humane endpoints Welfare-focused systematic review of surgical zebrafish models for cardiac regeneration Background Search strategy Study inclusion and exclusion criteria Results Mortality rates and speciesism Use of anaesthetics Conclusion: the state of zebrafish welfare today Acknowledgments References 6. Analgesia, anesthesia, and euthanasia in zebrafish Analgesia Opioids Morphine Buprenorphine Butorphanol Tramadol NSAIDs Aspirin Flunixin Ibuprofen Local anesthetics Lidocaine Bupivacaine Anesthesia MS-222 Benzocaine Clove oil Propofol Etomidate and metomidate Euthanasia Overdose of anesthetics Electrical stunning Rapid chilling Conclusions References 7. Transgenesis, mutagenesis, knockdown, and genetic colony management Introduction Ethical issues in genetic manipulation of laboratory fish Fish management during generation of mutants Mutant fish management Husbandry Health monitoring Quarantine provision and procedures Genotyping mutant lines to manage stocks Postresearch management for future opportunities and collaboration: cryopreservation and stock centers Data management Fish management during generation of transgenics Transgenic fish management Generation and management of morphants and CRISPants Management of CRISPants/morphants Conclusions Acknowledgments References 8. Sperm cryopreservation, in vitro fertilization, and embryo freezing Introduction Materials and methods Protocol for sperm cryopreservation and in vitro fertilization Collection and pooling of sperm Estimation of sperm cell densities and sample dilution Pooled sperm freezing Sperm motility assessment Egg collection Sperm sample thawing In vitro fertilization Protocol for embryo cryopreservation Zebrafish care and embryo collection Microinjection of CPA and GNR Use of a precooling bath Rapid cooling and laser warming Survival assessment Conclusion Acknowledgments References 9. Medaka as a model teleost: characteristics and approaches of genetic modification Medaka History of the medaka The medaka has been a popular pet in Japan History of the medaka as an experimental fish Husbandry and breeding under laboratory conditions Animal husbandry Breeding Husbandry during early larval stages Basic approaches of generation of transgenic/knockout medaka Conventional ways of introducing transgenes: plasmid/BAC-based constructs—their merits and demerits Generation of knockout using TALEN/CRISPR Double promoter methods for the efficient screening of transgenic lines Introduction of new transgenic methods Transgenesis with DNA transposase DNA transposon Transposase improves transgenic efficiency phiC31 integrase-mediated transgenesis Regarding phiC31 phiC31 integrase improves transgenic efficiency Advantage of phiC31 integrase The collection of attP-landing medaka strains Genetical features of attP-landing strains in the collection attB-targeting vector Advanced attB-targeting vector containing fluorescent protein for efficient screening in embryos Efficiency of phiC31-mediated transgenesis FLP recombinase-mediated locus cleanup Primer sequences to confirm integration by phiC31 integrase phiC31 integrase can be applicable to BAC/fosmid-based transgenesis Application of the highly efficient phiC31 integrase-based transgenesis for analysis of G0 generation An advantage and a basic principle of CRISPR/Cas-based knock-in approaches in medaka An efficient knock-in using a donor plasmid with bait sequences Pathways of DNA double-stranded break repair and their use for producing knock-in medaka Advantages, difficulties, and prospects for research on transgenic and genome editing in medaka Acknowledgment References 10. Integrated analyses using medaka as a powerful model animal toward understanding various aspects of reproductive regulation Medaka as a powerful model animal for research fields of reproduction Mechanisms of reproductive systems clarified by histological and physiological analyses Histological studies using medaka Immunohistochemistry In situ hybridization Single-cell labeling and tract tracing using axonal transport Conventional histological staining The present scheme of HPG axis regulation clarified by multidisciplinary analyses in vertebrates Differences between mammals and teleosts in terms of function of the kisspeptin neuronal system and HPG axis regulation Various novel functions of the kisspeptin neuronal system in teleosts Endocrine studies using medaka Surgery and blood sampling Hormonal analysis of sex steroid hormones Neurophysiological studies using medaka: patch clamp recording and calcium imaging Introduction to the neurophysiological analysis Neural activity analyzed by patch clamp recordings High-frequency firing of GnRH1 neuron in the afternoon stimulates LH cells Application of patch clamp recording to nonhypophysiotropic GnRH neurons Hormone/neuropeptide release clarified by Ca2+ imaging Neurophysiology advanced the understanding of neuroendocrinological regulation of reproduction Medaka provides clues to the understanding of general mechanisms of reproduction in teleosts and even in vertebrates Understanding of mechanism of HPG axis regulation in medaka and teleosts Difference of reproductive strategies and their underlying mechanisms—prolific teleosts and less prolific mammals Toward understanding of a general mechanism of neuroendocrine systems in vertebrates by taking advantage of medaka Acknowledgment References 11. The African turquoise killifish (Nothobranchius furzeri): biology and research applications Introduction Large-scale husbandry (including water systems and water parameters) Housing and water parameters Food Breeding strategies for genome engineering, including egg collection and incubation Breeding and embryo incubation for microinjection and genetic manipulation Breeding for maintenance Hatching of injected eggs and rearing of fry Reagent setup and additional protocols Embryo solution Coconut fiber preparation Humic acid preparation Disinfecting embryos by iodine Long-term storage of embryos and cryopreservation of sperm Receiving or shipping fertilized eggs Heat-shock protocol Efficient genome engineering approaches Target selection and synthesis of reagents for CRISPR/Cas9 genome editing Target selection gRNA template preparation Synthesis of gRNAs (1–2days) Synthesis of Cas9 mRNA (1–2days) Tol2-based transgenesis Microinjection Equipment setup Evaluation of editing efficiency (1–2days) Germline transmission and outcrosses Genotyping of adult fish Troubleshooting Fish dissection Experimental setup Organ dissection Body cavity dissection Trunk dissection Dissecting the head The African turquoise killifish: available toolbox “Omics” datasets Available genetic models Neurodegeneration and brain functions Cellular aging Physiological aging Diapause Summary and future perspectives Materials Reagents Equipment Acknowledgements References 12. Challenges in keeping annual killifish Introduction Available strains and species Housing and breeding Behavior and its association to welfare Types of killifish housing Water quality and sanitation Reproduction Embryo development Developmental diapauses Developmental variability Manipulation of embryo development in the laboratory Diet Diseases Velvet disease Glugea sp. infections Mycobacterioses Summary of the challenges Acknowledgments References 13. Mexican tetra (Astyanax mexicanus): biology, husbandry, and experimental protocols Biology and natural history Husbandry Housing Aggression behavior Nutrition and feeding Colony management Sexing Breeding and embryo handling Larviculture Animal welfare and health management Welfare indicators Health screening Common health issues Anesthesia Euthanasia Procedures Visible Implant Elastomer tagging Embryo dechorionation Gamete collection In vitro fertilization Injections Embryo microinjection Blood collection Oral gavage Cryopreservation Acknowledgments References Further reading 14. The housing, care, and use of a laboratory three-spined stickleback colony Introduction Supply, quarantine, and disinfection Source Arrival Basic husbandry Housing Environmental enrichment Stocking density and water quality Photoperiod and temperature Handling Feeding Feeding requirements First feeding and weaning Establishing and maintaining a successful colony Annual cycle of temperature and photoperiod Genitors and embryo production Sexual dimorphism Controlling sexual maturity and gamete production Natural breeding In vitro fertilization Embryo development On-growing Monitoring growth Procedures Blood sampling Spine clipping Genetic sex determination Conclusion Acknowledgments References 15. Goldfish (Carassius auratus): biology, husbandry, and research applications Taxonomy and phylogeny Morphology/anatomy External anatomy Internal anatomy Geography and natural habitat Behavior Social behavior Feeding behavior Reproductive behavior Husbandry Aquatic facility and housing Water quality Export and transportation Handling Feeding/nutrition Maintenance/cleaning and disinfection Breeding Diseases/pathogens/treatment Parasitic infections Ich/white spot disease Anchor worm Flukes Fish lice Velvet disease Trichodiniasis Costiasis Chilodonellasis Bacterial infections Fin rot Mouth rot Dropsy Pop eye Fungal infections Cotton wool Viral infections Carp pox Lymphocystis Other infections and diseases Swim bladder disorder Black spot disease Cloudy eye Hole-in-the-head disease Goldfish in biomedical research Regulation and policies Anesthesia, analgesia, and euthanasia Injections and blood collection Biomedical research applications Neuroscience Endocrinology, reproduction, and associated behaviors Toxicology and pharmacology Other use of goldfish in research Conclusions and perspectives References 16. Danionella translucida, a tankful of new opportunities Biology and ecology of Danionella translucida Neuroscience Development and evolution Animal husbandry: early larval stages Animal husbandry: early stages to adulthood Breeding Supplementary data Acknowledgments References Chapter-17---Fish-inventory-databas_2022_Laboratory-Fish-in-Biomedical-Resea 17. Fish inventory databases Introduction Basic operation principles Fish characterization and grouping Structure of a line name Animal grouping Record browsing and spatial tracking Tank labeling Performing actions and monitoring parameters Counting of the animals Animal age, productivity, and status Breeding management Monitoring of the conditions Temperature Light cycle Diet Water quality Other actions Statistics and reporting Advanced features User management Communication, requesting, and experiment planning Data management Examples of current solutions Commercial solutions PyRAT Aquatics (Scionics) Hybrid solutions Zebrabase (Oltova et al., 2018) Open-source solutions ZeBase (Hensley et al., 2012) Facile Fish (Yakulov and Walz, 2015) Future of fish databases Acknowledgment References Index A B C D E F G H I J K L M N O P Q R S T U V W X Y Z "Fish, particularly zebrafish, have become the fatest-growing segment of the research population. They offer several advantages in biology and applicable technologies and thus are employed in numerous research fields. Laboratory Fish in Biomedical Research: Biology, Husbandry and Research Applications for Zebrafish, Medaka, Killifish, Cavefish, Stickleback, Goldfish and Danionella translucida addresses the relevant, increasing need to collect cutting-edge knowledge on the most common freshwater species in terms of husbandry, maintenance, welfare, and experimental protocols under standard laboratory conditions. Key features: provides husbandry and management protocols, devices, and water systems; discusses strengths and weaknesses of breeding; explores potential scientific applications and experimental protocols of freshwater fish used the most in scientific endeavors."--Back cover