Fish is Fish: the use of experimental model species to reveal causes of skeletal diversity in evolution and disease

Weathered polyethylene microplastics induced immunomodulation in zebrafish

Microplastics are pollutants of emerging concern and the aquatic biota consumes microplastics (MPs), which has a range of toxicological and environmental effects on aquatic organisms that are not the intended targets. The current study looked into how weathered polyethylene (wPE) MPs affected Danio albolineatus immunological and haematological markers. In this experiment, fish of both sexes were placed in control and exposure groups, and they were exposed for 40 d at the sublethal level (1 μg L-1) of fragmented wPE, which contained 1074 ± 52 MPs per litre. Similarly, fish exposed to wPE MPs showed significant modifications in lysozyme, antimicrobial, and antiprotease activity, as well as differential counts. Results of the present study show that the male fish were more susceptible than female fish after 40 d of chronic exposure. Further studies are needed to ascertain how the innate and humoral immune systems of the fish respond to MPs exposure.

A cell line derived from heart of rainbow trout is refractory to Tilapia lake virus

Cell lines are important in vitro models to answer biological mechanisms with less genetic variations. The present study was attempted to develop a cell line from rainbow trout, where we obtained a cell line from the heart, named "RBT-H." The cell line was authenticated using karyotyping and cytochrome c oxidase subunit I (COI) gene sequencing. The karyotype demonstrated diploid chromosome number (2n) as 62 and the sequence of partial COI gene was 99.84% similar to rainbow trout COI data set, both suggesting the origin of RBT-H from the rainbow trout. The heart cell line was mycoplasma-free and found to be refractory to infection with the Tilapia lake virus. The RBT-H cell line is deposited in the National Repository of Fish Cell Line (NRFC) at ICAR-NBFGR, Lucknow, India, with Accession no. NRFC0075 for maintenance and distribution to researchers on request for R&D.

Exploring Omega-3's Impact on the Expression of Bone-Related Genes in Meagre (Argyrosomus regius)

Dietary supplementation with Omega-3 fatty acids seems to promote skeletal health. Therefore, their consumption at imbalanced or excessive levels has offered less beneficial or even prejudicial effects. Fish produced in aquaculture regimes are prone to develop abnormal skeletons. Although larval cultures are usually fed with diets supplemented with Omega-3 Long Chain Polyunsaturated fatty acids (LC-PUFAs), the lack of knowledge about the optimal requirements for fatty acids or about their impact on mechanisms that regulate skeletal development has impeded the design of diets that could improve bone formation during larval stages when the majority of skeletal anomalies appear. In this study, Argyrosomus regius larvae were fed different levels of Omega-3s (2.6% and 3.6% DW on diet) compared to a commercial diet. At 28 days after hatching (DAH), their transcriptomes were analyzed to study the modulation exerted in gene expression dynamics during larval development and identify impacted genes that can contribute to skeletal formation. Mainly, both levels of supplementation modulated bone-cell proliferation, the synthesis of bone components such as the extracellular matrix, and molecules involved in the interaction and signaling between bone components or in important cellular processes. The 2.6% level impacted several genes related to cartilage development, denoting a special impact on endochondral ossification, delaying this process. However, the 3.6% level seemed to accelerate this process by enhancing skeletal development. These results offered important insights into the impact of dietary Omega-3 LC-PUFAs on genes involved in the main molecular mechanism and cellular processes involved in skeletal development.

Zebrafish as a Model for Osteoporosis: Functional Validations of Genome-Wide Association Studies

PURPOSE OF REVIEW

GWAS, as a largely correlational analysis, requires in vitro or in vivo validation. Zebrafish (Danio rerio) have many advantages for studying the genetics of human diseases. Since gene editing in zebrafish has been highly valuable for studying embryonic skeletal developmental processes that are prenatally or perinatally lethal in mammalian models, we are reviewing pros and cons of this model.

RECENT FINDINGS

The true power for the use of zebrafish is the ease by which the genome can be edited, especially using the CRISPR/Cas9 system. Gene editing, followed by phenotyping, for complex traits such as BMD, is beneficial, but the major physiological differences between the fish and mammals must be considered. Like mammals, zebrafish do have main bone cells; thus, both in vivo stem cell analyses and in vivo imaging are doable. Yet, the "long" bones of fish are peculiar, and their bone cavities do not contain bone marrow. Partial duplication of the zebrafish genome should be taken into account. Overall, small fish toolkit can provide unmatched opportunities for genetic modifications and morphological investigation as a follow-up to human-first discovery.

Skeletal Morphogenesis and Anomalies in Gilthead Seabream: A Comprehensive Review

The gilthead seabream, one of the most important species in Mediterranean aquaculture, with an increasing status of exploitation in terms of production volume and aquafarming technologies, has become an important research topic over the years. The accumulation of knowledge from several studies conducted during recent decades on their functional and biological characteristics has significantly improved their aquacultural aspects, namely their reproductive success, survival, and growth. Despite the remarkable progress in the aquaculture industry, hatchery conditions are still far from ideal, resulting in frequent abnormalities at the beginning of intensive culture, entailing significant economic losses. Those deformities are induced during the embryonic and post-embryonic periods of life, and their development is still poorly understood. In the present review, we created a comprehensive synthesis that covers the various aspects of skeletal morphogenesis and anomalies in the gilthead seabream, highlighting the genetic, environmental, and nutritional factors contributing to bone deformities and emphasized the potential of the gilthead seabream as a model organism for understanding bone morphogenesis in both aquaculture and translational biological research. This review article addresses the existing lack in the literature regarding gilthead seabream bone deformities, as there are currently no comprehensive reviews on this subject.

Characterization of Fibrodysplasia Ossificans Progessiva relevant Acvr1/Acvr2 Activin receptors in medaka (Oryzias latipes)

Activin and Bone Morphogenetic Protein (BMP) signaling plays crucial roles in vertebrate organ formation, including osteo- and angiogenesis, and tissue homeostasis, such as neuronal maintenance. Activin and BMP signaling needs to be precisely controlled by restricted expression of shared receptors, stoichiometric composition of receptor-complexes and presence of regulatory proteins. A R206H mutation in the human (hs) BMP type I receptor hsACVR1, on the other hand, leads to excessive phosphorylation of Sons of mothers against decapentaplegic (SMAD) 1/5/8. This in turn causes increased inflammation and heterotopic ossification in soft tissues of patients suffering from Fibrodysplasia Ossificans Progressiva (FOP). Several animal models have been established to understand the spontaneous and progressive nature of FOP, but often have inherent limitations. The Japanese medaka (Oryzias latipes, ola) has recently emerged as popular model for bone research. To assess whether medaka is suitable as a potential FOP animal model, we determined the expression of Activin receptor type I (ACVR1) orthologs olaAcvr1 and olaAcvr1l with that of Activin type II receptors olaAcvr2ab, olaAcvr2ba and olaAcvr2bb in embryonic and adult medaka tissues by in situ hybridization. Further, we showed that Activin A binding properties are conserved in olaAcvr2, as are the mechanistic features in the GS-Box of both olaAcvr1 and olaAcvr1l. This consequently leads to FOP-typical elevated SMAD signaling when the medaka type I receptors carry the R206H equivalent FOP mutation. Together, this study therefore provides experimental groundwork needed to establish a unique medaka model to investigate mechanisms underlying FOP.

Impacts of microplastics on immunity

Most disposable plastic products are degraded slowly in the natural environment and continually turned to microplastics (MPs) and nanoplastics (NPs), posing additional environmental hazards. The toxicological assessment of MPs for marine organisms and mammals has been reported. Thus, there is an urgent need to be aware of the harm of MPs to the human immune system and more studies about immunological assessments. This review focuses on how MPs are produced and how they may interact with the environment and our body, particularly their immune responses and immunotoxicity. MPs can be taken up by cells, thus disrupting the intracellular signaling pathways, altering the immune homeostasis and finally causing damage to tissues and organs. The generation of reactive oxygen species is the mainly toxicological mechanisms after MP exposure, which may further induce the production of danger-associated molecular patterns (DAMPs) and associate with the processes of toll-like receptors (TLRs) disruption, cytokine production, and inflammatory responses in immune cells. MPs effectively interact with cell membranes or intracellular proteins to form a protein-corona, and combine with external pollutants, chemicals, and pathogens to induce greater toxicity and strong adverse effects. A comprehensive research on the immunotoxicity effects and mechanisms of MPs, including various chemical compositions, shapes, sizes, combined exposure and concentrations, is worth to be studied. Therefore, it is urgently needed to further elucidate the immunological hazards and risks of humans that exposed to MPs.

A Baseline for Skeletal Investigations in Medaka (Oryzias latipes): The Effects of Rearing Density on the Postcranial Phenotype

Oryzias latipes is increasingly used as a model in biomedical skeletal research. The standard approach is to generate genetic variants with particular skeletal phenotypes which resemble skeletal diseases in humans. The proper diagnosis of skeletal variation is key for this type of research. However, even laboratory rearing conditions can alter skeletal phenotypes. The subject of this study is the link between skeletal phenotypes and rearing conditions. Thus, wildtype medaka were reared from hatching to an early juvenile stage at low (LD: 5 individuals/L), medium (MD: 15 individuals/L), and high (HD: 45 individuals/L) densities. The objectives of the study are: (I) provide a comprehensive overview of the postcranial skeletal elements in medaka; (II) evaluate the effects of rearing density on specific meristic counts and on the variability in type and incidence of skeletal anomalies; (III) define the best laboratory settings to obtain a skeletal reference for a sound evaluation of future experimental conditions; (IV) contribute to elucidating the structural and cellular changes related to the onset of skeletal anomalies. The results from this study reveal that rearing densities greater than 5 medaka/L reduce the animals' growth. This reduction is related to decreased mineralization of dermal (fin rays) and perichondral (fin supporting elements) bone. Furthermore, high density increases anomalies affecting the caudal fin endoskeleton and dermal rays, and the preural vertebral centra. A series of static observations on Alizarin red S whole mount-stained preural fusions provide insights into the etiology of centra fusion. The fusion of preural centra involves the ectopic formation of bony bridges over the intact intervertebral ligament. An apparent consequence is the degradation of the intervertebral ligaments and the remodeling and reshaping of the fused vertebral centra into a biconoid-shaped centrum. From this study it can be concluded that it is paramount to take into account the rearing conditions, natural variability, skeletal phenotypic plasticity, and the genetic background along with species-specific peculiarities when screening for skeletal phenotypes of mutant or wildtype medaka.

Dynamics of the Zebrafish Skeleton in Three Dimensions During Juvenile and Adult Development

Zebrafish are a valuable model for normal vertebrate skeletogenesis and the study of myriad bone disorders. Bones grow, ossify and change shape throughout the zebrafish lifetime, and 3D technologies allow us to examine skeletogenic processes in detail through late developmental stages. To facilitate analysis of shape, orientation and tissue density of skeletal elements throughout ontogeny and adulthood, we generated a high-resolution skeletal reference dataset of wild-type zebrafish development. Using microCT technology, we produced 3D models of the skeletons of individuals ranging from 12 to 25 mm standard length (SL). We analyzed the dynamics of skeletal density and volume as they increase during juvenile and adult growth. Our resource allows anatomical comparisons between meristic units within an individual-e.g., we show that the vertebral canal width increases posteriorly along the spine. Further, structures may be compared between individuals at different body sizes: we highlight the shape changes that the lower jaw undergoes as fish mature from juvenile to adult. We show that even reproductively mature adult zebrafish (17-25 mm SL) continue to undergo substantial changes in skeletal morphology and composition with continued adult growth. We provide a segmented model of the adult skull and a series of interactive 3D PDFs at a range of key stages. These resources allow changes in the skeleton to be assessed quantitatively and qualitatively through late stages of development, and can serve as anatomical references for both research and education.

FELASA-AALAS Recommendations for Monitoring and Reporting of Laboratory Fish Diseases and Health Status, with an Emphasis on Zebrafish (Danio Rerio)

The exchange of fish for research may expose an aquatic laboratory to pathogen contamination as incoming fish can introduce bacteria, fungi, parasites, and viruses capable of affecting both experimental results and fish and personnel health and welfare. To develop risk mitigation strategies, FELASA and AALAS established a joint working group to recommend good practices for health monitoring of laboratory fish. The recommendations address all fish species used for research, with a particular focus on zebrafish (Danio rerio). First, the background of the working group and key definitions are provided. Next, fish diseases of high impact are described. Third, recommendations are made for health monitoring of laboratory fishes. The recommendations emphasize the importance of daily observation of the fish and strategies to determine fish colony health status. Finally, report templates are proposed for historical screening data and aquatic facility description to facilitate biohazard risk assessment when exchanging fish.

Zebrafish as a Vertebrate Model for Studying Nodavirus Infections

Nervous necrosis virus (NNV) is a neurotropic pathogenic virus affecting a multitude of marine and freshwater fish species that has a high economic impact on aquaculture farms worldwide. Therefore, the development of new tools and strategies aimed at reducing the mortality caused by this virus is a pivotal need. Although zebrafish is not considered a natural host for NNV, the numerous experimental advantages of this species make zebrafish an attractive model for studying different aspects of the disease caused by NNV, viral encephalopathy and retinopathy (VER). In this work, we established the best way and age to infect zebrafish larvae with NNV, obtaining significant mortalities in 3-day-postfertilization larvae when the virus was inoculated directly into the brain or by intramuscular microinjection. As occurs in naturally susceptible fish species, we confirmed that after intramuscular injection the virus was able to migrate to the central nervous system (CNS). As expected, due to the severe damage that this virus causes to the CNS, alterations in the swimming behavior of the zebrafish larvae were also observed. Taking advantage of the existence of transgenic fluorescent zebrafish lines, we were able to track the migration of different innate immune cells, mainly neutrophils, to the site of infection with NNV via the brain. However, we did not observe colocalization between the viral particles and neutrophils. RNA-Seq analysis of NNV-infected and uninfected larvae at 1, 3 and 5 days postinfection (dpi) revealed a powerful modulation of the antiviral immune response, especially at 5 dpi. We found that this response was dominated by, though not restricted to, the type I interferon system, the major defence mechanism in the innate immune response against viral pathogens. Therefore, as zebrafish larvae are able to develop the main characteristic of NNV infection and respond with an efficient immune arsenal, we confirmed the suitability of zebrafish larvae for modelling VER disease and studying different aspects of NNV pathogenesis, immune response and screening of antiviral drugs.

Polystyrene nanoplastics affect digestive function and growth in juvenile groupers

Polystyrene nanoplastics (PS-NPs) can impair antioxidant, immune, and nervous system functions as well as growth and development in aquatic organisms. At present, however, little is known about the effects and underlying mechanisms of PS-NPs on the digestive system of marine fish. Here, we studied the effects of these plastics on the intestinal health and growth performance of juvenile orange-spotted groupers (Epinephelus coioides). Based on histopathological analysis, we found that the liver and intestines can uptake PS-NPs at exposure concentrations of 300 and 3000 μg/ml, respectively. After 14 d of exposure, the activities of digestive enzymes lipase (LPS), trypsin (TRS), and lysozyme (LZM) were reduced, indicating that PS-NPs negatively affected digestive function in juvenile groupers. The PS-NPs also altered microbial community composition, resulting in a decrease in diversity and simplification of network relationships in the intestinal microbiota, but a significant increase in certain harmful bacteria, especially Vibrio and Aliivibrio. In addition, community assembly changed from being driven primarily by deterministic processes (68.89% for control group) to stochastic processes (73.33% and 51.11% for 300 and 3000 μg/ml PS-NP exposure groups, respectively). Furthermore, the specific growth rate (SGR) of the juvenile orange-spotted groupers decreased significantly with increasing PS-NP exposure concentrations (0.158% ± 0.032%, 0.095% ± 0.020%, and 0.074% ± 0.016% for 0, 300, and 3000 μg/L PS-NP groups, respectively). These results suggest that marine PS-NPs are harmful to the digestive system of juvenile fish and highlight the importance of evaluating the long-term impact of NPs in reshaping marine populations.

High-Resolution Histology for Craniofacial Studies on Zebrafish and Other Teleost Models

In the era of molecular biology, identification of cells and even tissues mostly relies on the presence of fluorescent tags, or of "marker gene" expression. We list a number of caveats and present a protocol for embedding, sectioning, and staining semithin plastic sections. The method is neither new nor innovative, but is meant to revive skills that tend to get lost.This easy-to-use and inexpensive protocol (1) yields high-resolution images in transmitted and polarized light, (2) can be utilized simultaneously for transmission electron microscopy, and (3) is applicable to any type of material (wild type, morphants, mutants, transgenic, or pharmacologically treated animals as well as all of their controls), provided the sample size is kept under a limit. Thus, we hope to encourage researchers to use microanatomy and histology to complement molecular studies investigating, e.g., gene function.

A comparison of the structure, composition and mechanical properties of anosteocytic vertebrae of medaka (O. latipes) and osteocytic vertebrae of zebrafish (D. rerio)

Medaka (O. latipes) and zebrafish (D. rerio) are two teleost fish increasingly used as models to study human skeletal diseases. Although they are similar in size, swimming pattern and many other characteristics, these two species are very distant from an evolutionary point of view (by at least 100 million years). A prominent difference between the skeletons of medaka and zebrafish is the total absence of osteocytes in medaka (anosteocytic), while zebrafish bone contains numerous osteocytes (osteocytic). This fundamental difference suggests the possibility that the bony elements of their skeleton may be different in a variety of other aspects, structural, mechanical or both, particularly in heavily loaded bones like the vertebrae. Here we report on the results of a comparative study that aimed to determine the similarities and differences in medaka and zebrafish vertebrae in terms of their macro- to nanostructure, composition and mechanical properties. Our results reveal many similarities between medaka and zebrafish vertebrae, making the lack or presence of osteocytes the only major difference between the bones of these two species.

Toxicity of silver nanoparticles on different tissues in adult Danio rerio

Although silver nanoparticles (AgNP) are among the most studied nanomaterials by virtue of their broad application in many areas, little is known about their overall toxicity to aquatic organisms after their contamination of the water environment. This study aimed to analyze the effect of the exposure (96 h) to different AgNP concentrations on Danio rerio (zebrafish) tissues. AgNP were synthesized and characterized by transmission electron microscopy (TEM), showing spherical AgNP of 30.00 ± 16.80 nm size. The effects of different AgNP concentrations (1, 3, and 5 μg L^-1) on brain, muscle, gill, and liver tissues of zebrafish were investigated. The results show a significant decrease in brain and muscle acetylcholinesterase (AChE) activity. Liver and gill catalase (CAT) activity also decreased significantly. At the highest exposure concentration, muscle AChE was more inhibited (37.3%) than brain AChE (26.4%) and gill CAT was more inhibited (67.4%) than liver CAT (51.2%). D. rerio also showed gill morphological changes such as fusion of secondary lamellae, curvature, dilated marginal channel, and epithelial lifting. This study indicates that gill CAT together with morphological studies are potential biomarkers for AgNP.

Radiological characterization of gilthead seabream (Sparus aurata) by X-ray computed tomography

In recent years, the increasing use of fish as new animal models in scientific research and the growth of fish farming (mainly for human consumption) have highlighted the need for advanced technology to deepen our knowledge of fish biology. Hence, the present study was carried out to radiologically analyse the whole body of gilthead seabream (Sparus aurata) specimens using X-ray computed tomography (CT). Images were acquired in an Albira SPECT/PET/CT tri-modal preclinical-scanner. Segmentation, measurements and three-dimensional reconstruction were made using the Carestream Molecular imaging Albira CT system in conjunction with Pmod, AMIDE and Amira software packages. The results showed that the density values of gilthead seabream are in the range -700 to +2500 HU for the whole body. We also determined the density ranges that topographically coincide with the swim bladder, soft tissues, fat, skin and skeleton. This work describes, validates and demonstrates the application of a fully automated image analysis technique to study and quantify fish body composition, whether segmented or as a whole. In addition, the basis for applying this image technique in other in vivo studies is established.

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

The FaceBase Consortium was established by the National Institute of Dental and Craniofacial Research in 2009 as a 'big data' resource for the craniofacial research community. Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community on the FaceBase Hub website. The Hub has developed numerous visualization and analysis tools designed to promote integration of multidisciplinary data while remaining dedicated to the FAIR principles of data management (findability, accessibility, interoperability and reusability) and providing a faceted search infrastructure for locating desired data efficiently. Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here. FaceBase 3 now welcomes contributions of data on craniofacial and dental development in humans, model organisms and cell lines. Collectively, the FaceBase Consortium, along with other NIH-supported data resources, provide a continuously growing, dynamic and current resource for the scientific community while improving data reproducibility and fulfilling data sharing requirements.

Zebrafish (Danio rerio) physiological and behavioural responses to insect-based diets: a multidisciplinary approach

Black Soldier Fly (BSF) meal is considered as an alternative, emerging and sustainable ingredient for aquafeed production. However, results on fish physiological responses are still fragmentary and often controversial, while no studies are available on fish behavior in response to these new diets. The present work represents the first comprehensive multidisciplinary study aimed to investigate zebrafish physiological and behavioural responses to BSF-based diets. Five experimental diets characterized by increasing inclusion levels (0, 25, 50, 75 and 100% respect to fish meal) of full fat BSF prepupae meal were tested during a 2-months feeding trial. Prepupae were cultured on coffee silverskin growth substrate enriched with a 10% Schizochytrium sp. to improve insects’ fatty acids profile. The responses of zebrafish were assayed through biometric, histological, gas chromatographic, microbiological, spectroscopic, molecular and behavioural analyses. Results evidenced that BSF-based diets affected fish fatty acid composition, while behavioural tests did not show differences among groups. Specifically, a 50% BSF inclusion level diet represented the best compromise between ingredient sustainability and proper fish growth and welfare. Fish fed with higher BSF inclusions (75 and 100%) showed hepatic steatosis, microbiota modification, higher lipid content, fatty acid modification and higher expression of immune response markers.

Evaluating fidelity of CT based 3D models for Zebrafish conductive hearing system

The zebrafish Weberian apparatus is an emerging model for human conductive hearing system. Their Weberian apparatus comprises minute bones and ligamentary links, and conducts sound pressure transmission from the gas bladder to inner ear through four pairs of Weberian ossicles along the vertebral column. We herein present a methodological study using MicroCT to image the Weberian apparatus for biomechanical and morphological analysis. The aim of this work is to evaluate computational models generated from multiple MicroCT scans with different parameters, to identify the most feasible scan combination for practical (minimized scan time) yet accurate (relative to highest resolution) biomechanical simulations. We segmented and created 3D models from CT scan image stacks at 4.64 μm, 5.05 μm, 9.30 μm and 13.08 μm voxel resolutions, respectively. Then, we used geometric morphometrics analysis to quantify inter-model shape differences, as well as a series of finite element modal and harmonic analyses to simulate auditory signal vibrations. Relative to the highest resolution and most accurate model, the Model 9.30 is closest in overall geometry and biomechanical behavior of all lower resolution models. The differences in resolution and quality of the CT substantially affect the segmentation and reconstruction process of the three-dimensional model of the ossicles, and the subsequent analyses. We conclude that scan voxel resolution is a key factor influencing outcomes of biomechanical simulations of delicate and minute structures, especially when studying the harmonic response of minute ossicles connected by ligaments using finite element modeling. Furthermore, contrast variations in CT images as determined by x-ray power and scan speed, also affect fidelity in 3D models and simulation outcomes.

A six-months study on Black Soldier Fly (Hermetia illucens) based diets in zebrafish

Intensive fish farming relies on the use of feeds based on fish meal and oil as optimal ingredients; however, further development of the aquaculture sector needs new, nutritious and sustainable ingredients. According to the concept of circular economy, insects represent good candidates as aquafeed ingredients since they can be cultured through environmental-friendly, cost-effective farming processes, on by-products/wastes, and many studies have recently been published about their inclusion in fish feed. However, information about the physiological effects of insect-based diets over the whole life cycle of fish is presently missing. At this regard, the present study investigated, for the first time, the effects of Black Soldier Fly based diets (25 and 50% fish meal substitution) administration for a six months period in zebrafish (Danio rerio), from larvae to adults. A multidisciplinary approach, including biometric, biochemical, histological, spectroscopic and molecular analyses was applied. Aside a general reduction in fish growth and lipid steatosis, six-months feeding on Black Soldier Fly based diets did not show major negative effects on zebrafish. Gut histological analysis on intestine samples did not show signs of inflammation and both stress markers and immune response markers did not show significant differences among the experimental groups.

Conserved but flexible modularity in the zebrafish skull: implications for craniofacial evolvability

Morphological variation is the outward manifestation of development and provides fodder for adaptive evolution. Because of this contingency, evolution is often thought to be biased by developmental processes and functional interactions among structures, which are statistically detectable through forms of covariance among traits. This can take the form of substructures of integrated traits, termed modules, which together comprise patterns of variational modularity. While modularity is essential to an understanding of evolutionary potential, biologists currently have little understanding of its genetic basis and its temporal dynamics over generations. To address these open questions, we compared patterns of craniofacial modularity among laboratory strains, defined mutant lines and a wild population of zebrafish (Danio rerio). Our findings suggest that relatively simple genetic changes can have profound effects on covariance, without greatly affecting craniofacial shape. Moreover, we show that instead of completely deconstructing the covariance structure among sets of traits, mutations cause shifts among seemingly latent patterns of modularity suggesting that the skull may be predisposed towards a limited number of phenotypes. This new insight may serve to greatly increase the evolvability of a population by providing a range of 'preset' patterns of modularity that can appear readily and allow for rapid evolution.

Zebrafish type I collagen mutants faithfully recapitulate human type I collagenopathies

The type I collagenopathies are a group of heterogeneous connective tissue disorders, that are caused by mutations in the genes encoding type I collagen and include specific forms of osteogenesis imperfecta (OI) and the Ehlers-Danlos syndrome (EDS). These disorders present with a broad disease spectrum and large clinical variability of which the underlying genetic basis is still poorly understood. In this study, we systematically analyzed skeletal phenotypes in a large set of zebrafish, with diverse mutations in the genes encoding type I collagen, representing different genetic forms of human OI, and a zebrafish model resembling human EDS, which harbors a number of soft connective tissues defects, typical of EDS. Furthermore, we provide insight into how zebrafish and human type I collagen are compositionally and functionally related, which is relevant in the interpretation of human type I collagen-related disease models. Our studies reveal a high degree of intergenotype variability in phenotypic expressivity that closely correlates with associated OI severity. Furthermore, we demonstrate the potential for select mutations to give rise to phenotypic variability, mirroring the clinical variability associated with human disease pathology. Therefore, our work suggests the future potential for zebrafish to aid in identifying unknown genetic modifiers and mechanisms underlying the phenotypic variability in OI and related disorders. This will improve diagnostic strategies and enable the discovery of new targetable pathways for pharmacological intervention.

The skeletal ontogeny of Astatotilapia burtoni - a direct-developing model system for the evolution and development of the teleost body plan

Background

The experimental approach to the evolution and development of the vertebrate skeleton has to a large extent relied on “direct-developing” amniote model organisms, such as the mouse and the chicken. These organisms can however only be partially informative where it concerns secondarily lost features or anatomical novelties not present in their lineages. The widely used anamniotes Xenopus and zebrafish are “indirect-developing” organisms that proceed through an extended time as free-living larvae, before adopting many aspects of their adult morphology, complicating experiments at these stages, and increasing the risk for lethal pleiotropic effects using genetic strategies.

Results

Here, we provide a detailed description of the development of the osteology of the African mouthbrooding cichlid Astatotilapia burtoni, primarily focusing on the trunk (spinal column, ribs and epicentrals) and the appendicular skeleton (pectoral, pelvic, dorsal, anal, caudal fins and scales), and to a lesser extent on the cranium. We show that this species has an extremely “direct” mode of development, attains an adult body plan within 2 weeks after fertilization while living off its yolk supply only, and does not pass through a prolonged larval period.

Conclusions

As husbandry of this species is easy, generation time is short, and the species is amenable to genetic targeting strategies through microinjection, we suggest that the use of this direct-developing cichlid will provide a valuable model system for the study of the vertebrate body plan, particularly where it concerns the evolution and development of fish or teleost specific traits. Based on our results we comment on the development of the homocercal caudal fin, on shared ontogenetic patterns between pectoral and pelvic girdles, and on the evolution of fin spines as novelty in acanthomorph fishes. We discuss the differences between “direct” and “indirect” developing actinopterygians using a comparison between zebrafish and A. burtoni development.

Identification of a fish short-chain dehydrogenase/reductase associated with bone metabolism

Although human and mouse genetics have largely contributed to the better understanding of the mechanisms underlying skeletogenesis, much more remains to be uncovered. In this regard alternative and complementary systems have been sought and cell systems capable of in vitro calcification have been developed to study the mechanisms underlying bone formation. In gilthead seabream (Sparus aurata), a gene coding for an unknown protein that is strongly up-regulated during extracellular matrix (ECM) mineralization of a pre-osteoblast cell line was recently identified as a potentially important player in bone formation. In silico analysis of the deduced protein revealed the presence of domains typical of short-chain dehydrogenase/reductases (SDR). Closely related to carbonyl reductase 1, seabream protein belongs to a novel subfamily of SDR proteins with no orthologs in mammals. Analysis of gene expression by qPCR confirmed the strong up-regulation of sdr-like expression during in vitro mineralization but also revealed high expression levels in calcified tissues. A possible role for Sdr-like in osteoblast and bone metabolism was further evidenced through (i) the localization by in situ hybridization of sdr-like transcript in pre-osteoblasts of the operculum and (ii) the regulation of sdr-like gene transcription by Runx2 and retinoic acid receptor, two regulators of osteoblast differentiation and mineralization. Expression data also indicated a role for Sdr-like in gastrointestinal tract homeostasis and during gilthead seabream development at gastrulation and metamorphosis. This study reports a new subfamily of short-chain dehydrogenases/reductases in vertebrates and, for the first time, provides evidence of a role for SDRs in bone metabolism, osteoblast differentiation and/or tissue mineralization.

Utility of quantitative micro-computed tomographic analysis in zebrafish to define gene function during skeletogenesis

The zebrafish is a powerful experimental model to investigate the genetic and morphologic basis of vertebrate development. Analysis of skeletogenesis in this fish is challenging as a result of the small size of the developing and adult zebrafish. Many of the bones of small fishes such as the zebrafish and medaka are quite thin, precluding many standard assays of bone quality and morphometrics commonly used on bones of larger animals. Microcomputed tomography (microCT) is a common imaging technique used for detailed analysis of the skeleton of the zebrafish and determination of mutant phenotypes. However, the utility of this modality for analysis of the zebrafish skeleton, and the effect of inherent variation among individual zebrafish, including variables such as sex, age and strain, is not well understood. Given the increased use and accessibility of microCT, we set out to define the sensitivity of microCT methods in developing and adult zebrafish. We assessed skeletal shape and density measures in the developing vertebrae and parasphenoid of the skull base. We found most skeletal variables are tightly correlated to standard length, but that at later growth stages (>3months) there are age dependent effects on some skeletal measures. Further we find modest strain but not sex differences in skeletal measures. These data suggest that the appropriate control for assessing mutant phenotypes should be age and strain matched, ideally a wild-type sibling. By analyzing two mutants exhibiting skeletal dysplasia, we show that microCT imaging can be a sensitive method to quantify distinct skeletal parameters of adults. Finally, as developing zebrafish skeletons remain difficult to resolve by radiographic means, we define a contrast agent specific for bone that enhances resolution at early stages, permitting detailed morphometric analysis of the forming skeleton. This increased capability for detection extends the use of this imaging modality to leverage the zebrafish model to understand the development causes of skeletal dysplasias.

Small teleost fish provide new insights into human skeletal diseases

Small teleost fish such as zebrafish and medaka are increasingly studied as models for human skeletal diseases. Efficient new genome editing tools combined with advances in the analysis of skeletal phenotypes provide new insights into fundamental processes of skeletal development. The skeleton among vertebrates is a highly conserved organ system, but teleost fish and mammals have evolved unique traits or have lost particular skeletal elements in each lineage. Several unique features of the skeleton relate to the extremely small size of early fish embryos and the small size of adult fish used as models. A detailed analysis of the plethora of interesting skeletal phenotypes in zebrafish and medaka pushes available skeletal imaging techniques to their respective limits and promotes the development of new imaging techniques. Impressive numbers of zebrafish and medaka mutants with interesting skeletal phenotypes have been characterized, complemented by transgenic zebrafish and medaka lines. The advent of efficient genome editing tools, such as TALEN and CRISPR/Cas9, allows to introduce targeted deficiencies in genes of model teleosts to generate skeletal phenotypes that resemble human skeletal diseases. This review will also discuss other attractive aspects of the teleost skeleton. This includes the capacity for lifelong tooth replacement and for the regeneration of dermal skeletal elements, such as scales and fin rays, which further increases the value of zebrafish and medaka models for skeletal research.

Xiphophorus and Medaka Cancer Models

Besides recently developed zebrafish cancer models, other fish species have been employed for many years as cancer models in laboratory studies. Two models, namely in Xiphophorus and medaka have proven useful in providing important clues to cancer etiology. Medaka is a complementary model to zebrafish in many areas of research since it offers similar resources and experimental tools. Xiphophorus provides the advantages of a natural ("evolutionary mutant") model with established genetics. Xiphophorus hybrids can develop spontaneous and radiation or carcinogen induced cancers. This chapter describes the tumor models in both species, which mainly focus on melanoma, and summarizes the main findings and future research directions.

Revisiting in vivo staining with alizarin red S--a valuable approach to analyse zebrafish skeletal mineralization during development and regeneration

BACKGROUND

The correct evaluation of mineralization is fundamental for the study of skeletal development, maintenance, and regeneration. Current methods to visualize mineralized tissue in zebrafish rely on: 1) fixed specimens; 2) radiographic and μCT techniques, that are ultimately limited in resolution; or 3) vital stains with fluorochromes that are indistinguishable from the signal of green fluorescent protein (GFP)-labelled cells. Alizarin compounds, either in the form of alizarin red S (ARS) or alizarin complexone (ALC), have long been used to stain the mineralized skeleton in fixed specimens from all vertebrate groups. Recent works have used ARS vital staining in zebrafish and medaka, yet not based on consistent protocols. There is a fundamental concern on whether ARS vital staining, achieved by adding ARS to the water, can affect bone formation in juvenile and adult zebrafish, as ARS has been shown to inhibit skeletal growth and mineralization in mammals.

RESULTS

Here we present a protocol for vital staining of mineralized structures in zebrafish with a low ARS concentration that does not affect bone mineralization, even after repetitive ARS staining events, as confirmed by careful imaging under fluorescent light. Early and late stages of bone development are equally unaffected by this vital staining protocol. From all tested concentrations, 0.01% ARS yielded correct detection of bone calcium deposits without inducing additional stress to fish.

CONCLUSIONS

The proposed ARS vital staining protocol can be combined with GFP fluorescence associated with skeletal tissues and thus represents a powerful tool for in vivo monitoring of mineralized structures. We provide examples from wild type and transgenic GFP-expressing zebrafish, for endoskeletal development and dermal fin ray regeneration.

Workshop report: The medaka model for comparative assessment of human disease mechanisms

Results of recent studies showing the utility of medaka as a model of various human disease states were presented at the 7th Aquatic Models of Human Disease Conference (December 13-18, 2014, Austin, TX). This conference brought together many of the most highly regarded national and international scientists that employ the medaka model in their investigations. To take advantage of this opportunity, a cohort of established medaka researchers were asked to stay an extra day and represent the medaka scientific community in a workshop entitled "The Medaka Model for Comparative Assessment of Human Disease Mechanisms." The central purpose of this medaka workshop was to assess current use and project the future resource needs of the American medaka research community. The workshop sought to spur discussions of issues that would promote more informative comparative disease model studies. Finally, workshop attendees met together to propose, discuss, and agree on recommendations regarding the most effective research resources needed to enable US scientists to perform experiments leading to impacting experimental results that directly translate to human disease. Consistent with this central purpose, the workshop was divided into two sessions of invited speakers having expertise and experience in the session topics. The workshop hosted 20 scientific participants (Appendices 1 and 2), and of these, nine scientists presented formal talks. Here, we present a summary report stemming from workshop presentations and subsequent round table discussions and forward recommendations from this group that we believe represent views of the overall medaka research community.

Power and challenges of using zebrafish as a model for skeletal tissue imaging

The zebrafish (Danio rerio) is now a widely used model organism in biomedical research. The species is also increasingly used for studying skeletal development and regeneration and for understanding human skeletal diseases. The small size of this model organism is an advantage and an extreme challenge for visualizing and diagnosing the animals' skeleton. This applies especially to early stages of skeletal development. Similar challenges arise for the analysis of the skeleton of other small fish species, such as medaka (Oryzias latipes). High quality histological preparations and knowledge about the special quality of the zebrafish skeleton remain prerequisites for a correct analysis. In addition, new methods for fast and high-resolution 2D and 3D skeletal tissue screening are required for a maximal understanding of skeletal development. We, in this study, review advantages and limitations of adapting current visualization techniques for zebrafish skeletal research. We discuss the methods for in toto visualization, such as X-raying, micro-CT, Alizarin red staining and optical projection tomography. Techniques for in vivo imaging, such as second harmonic generation microscopy and two-photon excitation fluorescence, are also discussed. Finally, we explore the possibilities of light-sheet microscopy for the analysis of the zebrafish skeleton.

Advancing biology through a deeper understanding of zebrafish ecology and evolution

Over the last two decades, the zebrafish has joined the ranks of premier model organisms for biomedical research, with a full suite of tools and genomic resources. Yet we still know comparatively little about its natural history. Here I review what is known about the natural history of the zebrafish, where significant gaps in our knowledge remain, and how a fuller appreciation of this organism's ecology and behavior, population genetics, and phylogeny can inform a variety of research endeavors.