Regular Care and Maintenance of a Zebrafish (Danio rerio) Laboratory: An Introduction

This protocol describes regular care and maintenance of a zebrafish laboratory. Zebrafish are now gaining popularity in genetics, pharmacological and behavioural research. As a vertebrate, zebrafish share considerable genetic sequence similarity with humans and are being used as an animal model for various human disease conditions. The advantages of zebrafish in comparison to other common vertebrate models include high fecundity, low maintenance cost, transparent embryos, and rapid development. Due to the spur of interest in zebrafish research, the need to establish and maintain a productive zebrafish housing facility is also increasing. Although literature is available for the maintenance of a zebrafish laboratory, a concise video protocol is lacking. This video illustrates the protocol for regular housing, feeding, breeding and raising of zebrafish larvae. This process will help researchers to understand the natural behaviour and optimal conditions of zebrafish husbandry and hence troubleshoot experimental issues that originate from the fish husbandry conditions. This protocol will be of immense help to researchers planning to establish a zebrafish laboratory, and also to graduate students who are intending to use zebrafish as an animal model.     

Blood collection for biochemical analysis in adult zebrafish

The zebrafish has been used as an animal model for studies of several human diseases. It can serve as a powerful preclinical platform for studies of molecular events and therapeutic strategies as well as for evaluating the physiological mechanisms of some pathologies. There are relatively few publications related to adult zebrafish physiology of organs and systems, which may lead researchers to infer that the basic techniques needed to allow the exploration of zebrafish systems are lacking. Hematologic biochemical values of zebrafish were first reported in 2003 by Murtha and colleagues who employed a blood collection technique first described by Jagadeeswaran and colleagues in 1999. Briefly, blood was collected via a micropipette tip through a lateral incision, approximately 0.3 cm in length, in the region of the dorsal aorta. Because of the minute dimensions involved, this is a high-precision technique requiring a highly skilled practitioner. The same technique was used by the same group in another publication in that same year. In 2010, Eames and colleagues assessed whole blood glucose levels in zebrafish. They gained access to the blood by performing decapitations with scissors and then inserting a heparinized microcapillary collection tube into the pectoral articulation. They mention difficulties with hemolysis that were solved with an appropriate storage temperature based on the work Kilpatrick et al. When attempting to use Jagadeeswaran's technique in our laboratory, we found that it was difficult to make the incision in precisely the right place as not to allow a significant amount of blood to be lost before collection could be started. Recently, Gupta et al. described how to dissect adult zebrafish organs, Kinkle et al. described how to perform intraperitoneal injections, and Pugach et al. described how to perform retro-orbital injections. However, more work is needed to more fully explore basic techniques for research in zebrafish. The small size of zebrafish presents challenges for researchers using it as an experimental model. Furthermore, given this smallness of scale, it is important that simple techniques are developed to enable researchers to explore the advantages of the zebrafish model.     

Dissection and Lateral Mounting of Zebrafish Embryos: Analysis of Spinal Cord Development

The zebrafish spinal cord is an effective investigative model for nervous system research for several reasons. First, genetic, transgenic and gene knockdown approaches can be utilized to examine the molecular mechanisms underlying nervous system development. Second, large clutches of developmentally synchronized embryos provide large experimental sample sizes. Third, the optical clarity of the zebrafish embryo permits researchers to visualize progenitor, glial, and neuronal populations. Although zebrafish embryos are transparent, specimen thickness can impede effective microscopic visualization. One reason for this is the tandem development of the spinal cord and overlying somite tissue. Another reason is the large yolk ball, which is still present during periods of early neurogenesis. In this article, we demonstrate microdissection and removal of the yolk in fixed embryos, which allows microscopic visualization while preserving surrounding somite tissue. We also demonstrate semipermanent mounting of zebrafish embryos. This permits observation of neurodevelopment in the dorso-ventral and anterior-posterior axes, as it preserves the three-dimensionality of the tissue.     

Modeling human muscle disease in zebrafish

Zebrafish reproduce in large quantities, grow rapidly, and are transparent early in development. For these reasons, zebrafish have been used extensively to model vertebrate development and disease. Like mammals, zebrafish express dystrophin and many of its associated proteins early in development and these proteins have been shown to be vital for zebrafish muscle stability. In dystrophin-null zebrafish, muscle degeneration becomes apparent as early as 3 days post-fertilization (dpf) making the zebrafish an excellent organism for large-scale screens to identify other genes involved in the disease process or drugs capable of correcting the disease phenotype. Being transparent, developing zebrafish are also an ideal experimental model for monitoring the fate of labeled transplanted cells. Although zebrafish dystrophy models are not meant to replace existing mammalian models of disease, experiments requiring large numbers of animals may be best performed in zebrafish. Results garnered from using this model could lead to a better understanding of the pathogenesis of the muscular dystrophies and the development of future therapies.     

Zebrafish embryos and larvae: a new generation of disease models and drug screens

Technological innovation has helped the zebrafish embryo gain ground as a disease model and an assay system for drug screening. Here, we review the use of zebrafish embryos and early larvae in applied biomedical research, using selected cases. We look at the use of zebrafish embryos as disease models, taking fetal alcohol syndrome and tuberculosis as examples. We discuss advances in imaging, in culture techniques (including microfluidics), and in drug delivery (including new techniques for the robotic injection of compounds into the egg). The use of zebrafish embryos in early stages of drug safety-screening is discussed. So too are the new behavioral assays that are being adapted from rodent research for use in zebrafish embryos, and which may become relevant in validating the effects of neuroactive compounds such as anxiolytics and antidepressants. Readouts, such as morphological screening and cardiac function, are examined. There are several drawbacks in the zebrafish model. One is its very rapid development, which means that screening with zebrafish is analogous to "screening on a run-away train." Therefore, we argue that zebrafish embryos need to be precisely staged when used in acute assays, so as to ensure a consistent window of developmental exposure. We believe that zebrafish embryo screens can be used in the pre-regulatory phases of drug development, although more validation studies are needed to overcome industry scepticism. Finally, the zebrafish poses no challenge to the position of rodent models: it is complementary to them, especially in early stages of drug research.     

The effect of excess expression of GFP in a novel heart-specific green fluorescence zebrafish regulated by nppa enhancer at early embryonic development

In order to study the impalpable effect of GFP in homozygous heart-specific GFP-positive zebrafish during the early stage, the researchers analyzed the heart function of morphology and physiology at the first 3 days after fertilization. This zebrafish line was produced by a large-scale Tol2 transposon mediated enhancer trap screen that generated a transgenic zebrafish with a heart-specific expression of green fluorescent protein (GFP)-tagged under control of the nppa enhancer. In situ hybridization experiments showed that the nppa:GFP line faithfully recapitulated both the spatial and temporal expressions of the endogenous nppa. Green fluorescence was intensively and specifically expressed in the myocardial cells located both in the heart chambers and in the atrioventricular canal. The embryonic heart of nppa:GFP line developed normally compared with those in the wild type. There was no difference between the nappa:GFP and wild type lines with respect to heart rate, overall size, ejection volume, and fractional shortening. Thus the excess expression of GFP in this transgenic line seemed to exert no detrimental effects on zebrafish hearts during the early stages.     

台湾地区斑马鱼研究现况

台湾地区斑马鱼研究起始于1996年,在经历了约8年的萌芽期(1996~2003年)之后,目前已进入到茁壮期(2004~现今),现今全台湾共有83个实验室使用斑马鱼作为实验材料,台湾地区斑马鱼研究社群的研究主题可大致分成3大类:(1)胚胎发育;(2)人类疾病;(3)生物技术。累积至今与斑马鱼相关论文发表总数已达到342篇。自2010年起,台湾也成立了两个斑马鱼种质资源库(TZCAS与ZeTH)。在种质资源库的充分协助下,目前许多医院的临床医师、工程与生物信息相关领域的研究人员,也开始加入斑马鱼研究社群进行跨领域的整合性研究,成为现今台湾地区斑马鱼研究的一大特色。     

水平回转培养对斑马鱼血管发育的影响

随着空间生命科学的发展, 微重力对生命体的影响已成为科学家们日益关注的问题。多数研究表明, 微重力对生物体胚胎早期发育有着重要影响, 而血管系统作为胚胎最早行使功能的系统备受关注。目前关于微重力对血管发育影响的研究大多来自对离体培养细胞的体外回转模拟实验, 在体实验相对较少。文章利用斑马鱼作为模式动物, 在体探究水平回转培养环境下斑马鱼胚胎早期发育及水平回转培养对其血管系统发育的影响。在斑马鱼受精后24 h(24 hpf)时进行水平回转培养处理, 至36 hpf时收集胚胎, 通过体视显微镜观察斑马鱼表型变化, 通过半定量RT-PCR、qPCR及全胚原位杂交等手段对比水平回转培养环境下与对照组血管相关因子的表达情况, 并通过BrdU掺入及TUNEL法进行斑马鱼全胚细胞凋亡及增殖检测。结果表明, 在90 r/min水平回转培养环境下, 斑马鱼死亡数量没有差异, 24 hpf时破壳数量显著降低(10.3±0.41 vs. 0.0, P<0.05), 心率显著加快(223.5±2.32 vs. 185.0±3.23, P<0.05), 黑色素明显增加, 动静脉发育紊乱, 且在120 r/min转速下, 胚胎血管特异性表达因子flk1、flt4及 ephrinB2的表达均显著降低, 斑马鱼细胞凋亡明显增加, 而细胞增殖无显著差异, 提示水平回转培养对斑马鱼胚胎发育特别是早期血管发育具有重要影响。     

基于Cytoscape下斑马鱼衰老基因-蛋白质的模块化分析

近20年来,斑马鱼逐渐成为研究人类基因功能的重要模型动物。同时,通过对斑马鱼参考基因组序列和10 000多个蛋白编码基因的鉴定,表明斑马鱼至少与人类基因有75%的同源性,进一步验证了斑马鱼基因组序列可以作为衰老的研究模型。此外,其良好保守的分子和细胞生理学的广泛特征使斑马鱼成为揭示衰老、疾病和修复的潜在机制的极好模型。但是斑马鱼衰老的分子机制很少发生分子间的相互作用,因此蛋白质-蛋白相互作用(PPI)网络是非常可取的。本实验描述了斑马鱼这种生物衰老机制的模型,其涵盖了与衰老相关的87种蛋白质之间的767种相互作用。这不仅包含准确预测的PPI,还包含从文献收集以及实验所得的那些分子相互作用。同时,将这些分子相互作用模块化,形成模块化,找到11个中心基因,分析预测其衰老过程。希望能帮助研究斑马鱼的学者研究其衰老过程,提供一些假说和帮助。     

The zebrafish brain in research and teaching: a simple in vivo and in vitro model for the study of spontaneous neural activity

Recently, the zebrafish (Danio rerio) has been established as a key animal model in neuroscience. Behavioral, genetic, and immunohistochemical techniques have been used to describe the connectivity of diverse neural circuits. However, few studies have used zebrafish to understand the function of cerebral structures or to study neural circuits. Information about the techniques used to obtain a workable preparation is not readily available. Here, we describe a complete protocol for obtaining in vitro and in vivo zebrafish brain preparations. In addition, we performed extracellular recordings in the whole brain, brain slices, and immobilized nonanesthetized larval zebrafish to evaluate the viability of the tissue. Each type of preparation can be used to detect spontaneous activity, to determine patterns of activity in specific brain areas with unknown functions, or to assess the functional roles of different neuronal groups during brain development in zebrafish. The technique described offers a guide that will provide innovative and broad opportunities to beginner students and researchers who are interested in the functional analysis of neuronal activity, plasticity, and neural development in the zebrafish brain.     

Considering the zebrafish in a comparative context

This article introduces a special issue on zebrafish biology that attempts to integrate developmental genetics with comparative studies of other fish species. For zebrafish researchers, comparative work offers a better understanding of the evolutionary history of their model system. Comparative biologists can gain many insights from the developmental and genetic mechanisms revealed in zebrafish that have contributed to the huge range of morphological variation among fishes that has arisen over millions of years. These ideas are considered here in various contexts, including systematics, genome organization and the development of the nervous system, pigmentation, craniofacial skeleton and dentition. Studies of the zebrafish in phylogenetic context provide an opportunity for synergy between communities using these two fundamentally different approaches.     

Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in-vitro culture in cryopreservation studies

Development of in vitro culture protocol for early stage ovarian follicles of zebrafish is important since cryopreserved early stage ovarian follicles would need to be matured in vitro following cryopreservation before they can be fertilised. Development of molecular markers for zebrafish (Danio rerio) ovarian follicle growth assessment following in vitro culture of early stage zebrafish ovarian follicles in ovarian tissue fragments is reported here for the first time although some work has been reported for in vitro culture of isolated early stage zebrafish ovarian follicles. The main aim of the present study was to develop molecular markers in an optimised in vitro culture protocol for stage I and stage II zebrafish ovarian follicles in ovarian tissue fragments. The effect of concentration of the hormones human chorionic gonadotropin and follicle stimulating hormones, and additives such as Foetal Bovine Serum and Bovine Serum Albumin were studied. The results showed that early stage zebrafish ovarian fragments containing stage I and stage II follicles which are cultured in vitro for 24 h in 20% FBS and 100mIU/ml FSH in 90% L-15 medium at 28 °C can grow to the size of stage II and stage III ovarian follicles respectively. More importantly the follicle growth from stage I to stage II and from stage II to stage III were confirmed using molecular markers such as cyp19a1a (also known as P450aromA) and vtg1 genes respectively. However, no follicle growth was observed following cryopreservation and in vitro culture.     

Immunological detection of changes in genomic DNA methylation during early zebrafish development.

DNA methylation reprogramming, the erasure of DNA methylation patterns shortly after fertilization and their reestablishment during subsequent early development, is essential for proper mammalian embryogenesis. In contrast, the importance of this process in the development of non-mammalian vertebrates such as fish is less clear. Indeed, whether or not any widespread changes in DNA methylation occur at all during cleavage and blastula stages of fish in a fashion similar to that shown in mammals has remained controversial. Here we have addressed this issue by applying the techniques of Southwestern immunoblotting and immunohistochemistry with an anti-5-methylcytosine antibody to the examination of DNA methylation in early zebrafish embryos. These techniques have recently been utilized to demonstrate that development-specific changes in genomic DNA methylation also occur in Drosophila melanogaster and Dictyostelium discoideum, both organisms for which DNA methylation was previously not thought to occur. Our data demonstrate that genome-wide changes in DNA methylation occur during early zebrafish development. Although zebrafish sperm DNA is strongly methylated, the zebrafish genome is not detectably methylated through cleavage and early blastula stages but is heavily remethylated in blastula and early gastrula stages.     

Animal models of human disease: zebrafish swim into view

Despite the pre-eminence of the mouse in modelling human disease, several aspects of murine biology limit its routine use in large-scale genetic and therapeutic screening. Many researchers who are interested in an embryologically and genetically tractable disease model have now turned to zebrafish. Zebrafish biology allows ready access to all developmental stages, and the optical clarity of embryos and larvae allow real-time imaging of developing pathologies. Sophisticated mutagenesis and screening strategies on a large scale, and with an economy that is not possible in other vertebrate systems, have generated zebrafish models of a wide variety of human diseases. This Review surveys the achievements and potential of zebrafish for modelling human diseases and for drug discovery and development.     

Cloning and expression of zebrafish neuronal nicotinic acetylcholine receptors

We propose to use the zebrafish (Danio rerio) as a vertebrate model to study the role of neuronal nicotinic acetylcholine receptors (nAChR) in development. As a first step toward using zebrafish as a model, we cloned three zebrafish cDNAs with a high degree of sequence similarity to nAChR beta3, alpha2 and alpha7 subunits expressed in other species. RT-PCR was used to show that the beta3 and alpha2 subunit RNAs were present in zebrafish embryos only 2-5hours post-fertilization (hpf) while alpha7 subunit RNA was not detected until 8hpf, supporting the differential regulation of nAChRs during development. In situ hybridization was used to localize zebrafish beta3, alpha2, and alpha7 RNA expression. nAChR binding techniques were used to detect the early expression of two high-affinity [3H]-epibatidine binding sites in 2 days post-fertilization (dpf) zebrafish embryos with IC(50) values of 28.6pM and 29.7nM and in 5dpf embryos with IC(50) values of 28.4pM and 8.9nM. These studies are consistent with the involvement of neuronal nAChRs in early zebrafish development.     

斑马鱼NUP98基因的克隆及其时空表达图谱

目的：斑马鱼NUP98基因的克隆及其在个体早期发育过程中的表达情况研究。方法：提取斑马鱼胚胎的总RNA,制备地高辛标记的NUP98RNA反义探针,WISH（整体胚胎原位杂交）研究NUP98在斑马鱼早期发育过程中的表达;提取斑马鱼胚胎各时相和成鱼各组织的RNA,实时定量PCR检测斑马鱼胚胎各时相和成鱼各组织中的表达。结果：成功克隆斑马鱼NUP98基因,通过实时定量RT-PCR和原位杂交,获得NUP98基因在斑马鱼早期发育过程中的表达情况：NUP98在2-cell、32．cell、oblong、shield期、12h前普遍性表达（0．75h、1．7h、3．7h、6h、12h）;24h以后在眼部、头部表达较多,特别是在脊索表达较高;斑马鱼NUP98在0、0．5h、6h、12h、24h、48h表达逐渐降低,到72h和96h表达有所增加,但是仍低于24h其表达水平;NUP98在成鱼眼、脑、鳔、肾、肝、睾丸、胆囊、卵巢、鳍、心、肠、肌肉、腮、皮肤的表达中,眼的表达最高,明显高于其他组织,腮、卵巢、肠的表达次之,肌肉、鳔、胆囊、睾丸、皮肤、脑的表达紧随其后,鳍、肝、心、肾的表达最低。结论：NUP98基因可能在个体脑部、脊索及眼部的早期发育过程中起到了重要作用;NUP98基因可能具有抑制肿瘤发生的作用,该基因的调节异常对白血病的发生发展可能有重要影响。这些研究结果为进一步研究NUP98基因在造血系统中的作用,评估其是否适合作为血液系统恶性肿瘤的新的治疗靶点等奠定了理论基础。     

Diagnostic techniques for clinical investigation of laboratory zebrafish

Unexpected morbidity and mortality of aquatic animal models represent a significant problem for researchers. The authors outline the basic procedures used to diagnose disease outbreaks in laboratory zebrafish colonies, and provide a basic framework for initiating clinical investigations.