Zebrafish is recognized as one of the most important vertebrate model organisms; however, its value in pharmacological studies has not been extensively explored and exploited. In this review, I summarize significant findings about the effects of drugs and medicines on important physiological processes in zebrafish. Our experiments have shown that cardiovascular, anti‐angiogenic and anti‐cancer drugs elicit comparable responses in zebrafish embryos to those in mammalian systems. Similar observations have been reported by other laboratories, exposing zebrafish to (...) a variety of pharmaceutical active compounds affecting a range of different processes. All the data summarized indicate that zebrafish represents a very valuable organism for different kinds of pharmacological studies, such as screenings of chemical libraries, lead validation and optimization, mode‐of‐action studies, analysis of gene function, predictive toxicology and teratogenicity, pharmacogenomics and toxicogenomics. Zebrafish pharmacological assays have specific advantages compared to in vitro cell culture studies and in vivo experiments using mice, complementing these assays to give valuable guides for future tests of new drugs for human therapy. BioEssays 25:904–912, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

Development of the vertebrate pancreas is a complex stepwise process comprising regionalization, cell differentiation, and morphogenesis. Studies in zebrafish are contributing to an emerging picture of pancreas development in which extrinsic signaling molecules influence intrinsic transcriptional programs to allow ultimate differentiation of specific pancreatic cell types. Zebrafish experiments have revealed roles for several signaling molecules in aspects of this process; for example our own work has shown that retinoic acid signals specify the pre‐pancreatic endoderm. Time‐lapse imaging of live (...) zebrafish embryos has started to provide detailed information about early pancreas morphogenesis. In addition to modeling embryonic development, the zebrafish has recently been used as a model for pancreas regeneration studies. Here, we review the significant progress in these areas and consider the future potential of zebrafish as a diabetes research model. (shrink)

Skin pigment pattern formation is a paradigmatic example of pattern formation. In zebrafish, the adult body stripes are generated by coordinated rearrangement of three distinct pigment cell‐types, black melanocytes, shiny iridophores and yellow xanthophores. A stem cell origin of melanocytes and iridophores has been proposed although the potency of those stem cells has remained unclear. Xanthophores, however, seemed to originate predominantly from proliferation of embryonic xanthophores. Now, data from Singh et al. shows that all three cell‐types derive from shared (...) stem cells, and that these cells generate peripheral neural cell‐types too. Furthermore, clonal compositions are best explained by a progressive fate restriction model generating the individual cell‐types. The numbers of adult pigment stem cells associated with the dorsal root ganglia remain low, but progenitor numbers increase significantly during larval development up to metamorphosis, likely via production of partially restricted progenitors on the spinal nerves. (shrink)

Claudins serve essential roles in regulating paracellular permeability properties within occluding junctions. Recent studies have begun to elucidate developmental roles of claudins within immature tissues. This work has uncovered an involvement of several claudins in determining tight junction properties that have an effect on embryonic morphogenesis and physiology. During zebrafish brain morphogenesis, Claudin‐5a determines the paracellular permeability of tight junctions within a transient neuroepithelial‐ventricular barrier that maintains the hydrostatic fluid pressure required for brain ventricular lumen expansion. However, the roles (...) of Claudins in development may well extend beyond being mere junctional components. Several post‐translational modifications of Claudins have been characterized that indicate a direct regulation by developmental signals. This review focuses on the involvement of Claudin‐5a in cerebral barrier formation in the zebrafish embryo and includes some speculations about possible modes of regulation. (shrink)

Model organisms became an indispensable part of experimental systems in molecular developmental and cell biology, constructed to investigate physiological and pathological processes. They are thought to play a crucial role for the elucidation of gene function, complementing the sequencing of the genomes of humans and other organisms. Accordingly, historians and philosophers paid considerable attention to various issues concerning this aspect of experimental biology. With respect to the representational features of model organisms, that is, their status as models, the main focus (...) was on generalization of phenomena investigated in such experimental systems. Model organisms have been said to be models for other organisms or a higher taxon. This, however, presupposes a representation of the phenomenon in question. I will argue that prior to generalization, model organisms allow researchers to built generative material models of phenomena – structures, processes or the mechanisms that explain them – through their integration in experimental set-ups that carve out the phenomena from the whole organism and thus represent them. I will use the history of zebrafish biology to show how model organism systems, from around 1970 on, were developed to construct material models of molecular mechanisms explaining developmental or physiological processes. (shrink)

The identification of molecules controlling embryonic patterning and their functional analysis has revolutionized the fields of Developmental and Cell Biology. The use of new sequence information and modern bioinformatics tools has enriched the list of proteins that could potentially play a role in regulating cell behavior and function during early development. The recent application of efficient methods for gene knockout in zebrafish has accelerated the functional analysis of many proteins, some of which have been overlooked due to their small (...) size. Two recent publications report on the identification of one such protein and its role in zebrafish embryogenesis. The protein, currently designated Apela, was shown to act as a secreted protein whose absence adversely affected various early developmental processes. Additional signaling proteins that have been identified in one of the studies are likely to open the way to unraveling hitherto unknown developmental pathways and have the potential to provide a more comprehensive understanding of known developmental processes. (shrink)

Animal personality refers to the consistency of variation in behavior among individuals which may be the driving force behind variations in complex behaviors as well. Individual personality could predict how well an organism would perform in behavior and cognition related tasks, as well as survive and thrive in its environment. Therefore, we would expect inter-individual variations in many behaviors, which would persist even if habituation to the experimental setup occurs, which generally results in convergence of behavior. Our study used wild-caught (...) zebrafish from three natural habitats with differing ecological regimes, to understand how consistency and repeatability in specific traits such as boldness, exploration, and spatial ability varies across and within populations even when habituation causes change in behavior. We found that the extent of individual variation differs between populations, with dynamic habitats showing similar repeatability. This indicates that habitat conditions are important drivers of individual variation in addition to other factors, such as sex or size of individuals within populations. Although we found that sex and size played an important role within some populations for some behaviors, in others, the variation was likely caused by other factors, for which we have not accounted. This study underlines the importance of studying inter-individual differences as the phenomenon that underpins multiple behavioral traits and explains the possible role of environmental and inherent factors that drive these differences. (shrink)

Vascular development entails multiple cell‐fate decisions to specify a diverse array of vascular structures. Notch proteins are signaling receptors that regulate cell‐fate determination in a variety of cell types. The finding that Notch genes are robustly expressed in the vasculature suggests roles for Notch in guiding endothelial and associated mural cells through the myriad of cell‐fate decisions needed to form the vasculature. In fact, mice with defects in genes encoding Notch, Notch ligands, and components of the Notch signaling cascade invariably (...) display vascular defects. Human Notch genes are linked to Alagille's Syndrome, a developmental disorder with vascular defects, and CADASIL, a cerebral arteriopathy. Studies in zebrafish, mice and humans indicate that Notch works in conjunction with other angiogenic pathways to pattern and stabilize the vasculature. Here, we will focus on established functions for Notch in vascular remodeling and arterial/venous specification and more speculative roles in vascular homeostasis and organ‐specific angiogenesis. BioEssays 26:225–234, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

We propose to study the wound healing in Zebrafish by using firstly a differential approach for modelling morphogens diffusion and cell chemotactic motion, and secondly a hybrid model of tissue regeneration, where cells are considered as individual objects and molecular concentrations are described by partial differential equations.

Development of an animal embryo involves the coordination of cell divisions, a variety of inductive interactions and extensive cellular rearrangements. One of the biggest challenges in developmental biology is to explain the relationships between these processes and the mechanisms that regulate them. Teleost embryos provide an ideal subject for the study of these issues. Their optical lucidity combined with modern techniques for the marking and observation of individual living cells allow high resolution investigations of specific morphogenetic movements and the construction (...) of detailed fate maps. In this review we describe the patterns of cell divisions, cellular movements and other morphogenetic events during zebrafish early development and discuss how these events relate to the formation of restricted lineages. (shrink)

Most organisms display oscillations of approximately 24 hours in their physiology. In higher organisms, these circadian oscillations in biochemical and physiological processes ultimately control complex behavioral rhythms that allow an organism to thrive in its natural habitat. Daily and seasonal light cycles are mainly responsible for keeping the circadian system properly aligned with the environment. The molecular mechanisms responsible for the control of the circadian clock have been explored in a number of systems. Interestingly, the circadian oscillations that are responsive (...) to environmental stimuli are present very early during development. This review focuses on the advantages of using the zebrafish to study the development of the vertebrate circadian system and light‐dependent signaling to the clock. BioEssays 24:419–426, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Teeth are one of the most fascinating innovations of vertebrates. Their diversity of shape, size, location, and number in vertebrates is astonishing. If the molecular mechanisms underlying the morphogenesis of individual teeth are now relatively well understood, thanks to the detailed experimental work that has been performed in model organisms (mainly mouse and zebrafish), the mechanisms that control the organization of the dentition are still a mystery. Mammals display simplified dentitions when compared to other vertebrates with only a single (...) tooth row positioned in the anterior part of the mouth, whereas other vertebrates exhibit tooth rows in many locations. As proposed 60 years ago, tooth rows can be formed sequentially from an initiator tooth. Recent results in zebrafish have now largely confirmed this hypothesis. Here this observation is generalized upon and it is suggested that in most vertebrates tooth rows could form sequentially from a single initiator tooth. (shrink)

Regenerative medicine promises to greatly impact on human health by improving repair outcomes in a range of tissues and injury contexts. Successful therapies will rely on identifying both intrinsic and extrinsic biological circuits that control wound healing, proliferation, cell survival, and developmental cell fate. Animals such as the zebrafish and the salamander display powerful examples of near‐perfect regeneration and scar‐free healing in a range of injury contexts not attained in mammals. By studying regeneration in a range of highly regenerative (...) species that maintain regenerative potential throughout life, many instructive and permissive factors have been identified that could assist in the development of regenerative therapies. This review highlights some of the recent observations in immune regulation, epigenetic regulation, stem cell mobilization, and regenerative signatures that have improved our understanding of the regenerative process. Potential opportunities in harnessing this knowledge for future translation into the clinic are discussed. (shrink)

Adult stem cell populations must coordinate their own maintenance with the generation of differentiated cell types to sustain organ physiology, in a spatially controlled manner and over long periods. Quantitative analyses of clonal dynamics have revealed that, in epithelia, homeostasis is achieved at the population rather than at the single stem cell level, suggesting that feedback mechanisms coordinate stem cell maintenance and progeny generation. In the central nervous system, however, little is known of the possible community processes underlying neural stem (...) cell maintenance. Recent work, in part based on intravital imaging made possible in the adult zebrafish, conclusively highlights that homeostasis in neural stem cell pools may rely on population asymmetry and long‐term spatiotemporal coordination of neural stem cell states and fates. These results suggest that neural stem cell assemblies in the vertebrate brain behave as self‐organized systems, such that the stem cells themselves generate their own intrinsic niche. (shrink)

Vertebrates respond to light with more than just their eyes. In this article, we speculate on the intriguing possibility that a link remains between non‐visual opsins and neurohormonal systems that control neuronal circuit formation and activity in mammals. Historically, the retina and pineal gland were considered the only significant light‐sensing tissues in vertebrates. However over the last century, evidence has accumulated arguing that extra‐ocular tissues in vertebrates influence behavior through non‐image‐forming photoreception. One such class of extra‐ocular light detectors are the (...) long mysterious deep brain photoreceptors. Here, we review recent findings on the cellular identity and the function of deep brain photoreceptors controlling behavior and physiology in zebrafish, and discuss their implications. (shrink)

Vertebrates respond to light with more than just their eyes. In this article, we speculate on the intriguing possibility that a link remains between non‐visual opsins and neurohormonal systems that control neuronal circuit formation and activity in mammals. Historically, the retina and pineal gland were considered the only significant light‐sensing tissues in vertebrates. However over the last century, evidence has accumulated arguing that extra‐ocular tissues in vertebrates influence behavior through non‐image‐forming photoreception. One such class of extra‐ocular light detectors are the (...) long mysterious deep brain photoreceptors. Here, we review recent findings on the cellular identity and the function of deep brain photoreceptors controlling behavior and physiology in zebrafish, and discuss their implications. (shrink)

Over the past decade, high‐throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non‐coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of (...) translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein‐encoding mRNAs to potentially non‐functional peptide‐producing RNAs to non‐coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela/ELABELA/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts. (shrink)

We developed an ex silico evolutionary‐based systematic synteny approach to define and name the duplicated genes in vertebrates. The first convention for the naming of genes relied on historical precedent, the order in the human genome, and mutant phenotypes in model systems. However, total‐genome duplication that resulted in teleost genomes required the naming of duplicated orthologous genes (ohnologs) in a specific manner. Unfortunately, as we review here, such naming has no defined criteria, and some ohnologs and their orthologs have suffered (...) from incorrect nomenclature, thus creating confusion in comparative genetics and disease modeling. We sought to overcome this barrier by establishing an ex silico evolutionary‐based systematic approach to naming ohnologs in teleosts. We developed software and compared gene synteny in zebrafish using the spotted gar genome as a reference, representing the unduplicated ancestral state. Using new criteria, we identified several hundred potentially misnamed ohnologs and validated the principle manually. Also see the video abstract here: https://youtu.be/UKNLa_TvSgY. (shrink)

Abnormalities in the ability of cells to properly degrade proteins have been identified in many neurodegenerative diseases. Recent work has implicated synaptojanin 1 (SynJ1) in Alzheimer's disease and Parkinson's disease, although the role of this polyphosphoinositide phosphatase in protein degradation has not been thoroughly described. Here, we dissected in vivo the role of SynJ1 in endolysosomal trafficking in zebrafish cone photoreceptors using a SynJ1‐deficient zebrafish mutant, nrca14. We found that loss of SynJ1 leads to specific accumulation of late (...) endosomes and autophagosomes early in photoreceptor development. An analysis of autophagic flux revealed that autophagosomes accumulate because of a defect in maturation. In addition we found an increase in vesicles that are highly enriched for PI(3)P, but negative for an early endosome marker in nrca14 cones. A mutational analysis of SynJ1 enzymatic domains found that activity of the 5'phosphatase, but not the Sac1 domain, is required to rescue both aberrant late endosomes and autophagosomes. Finally, modulating activity of the PI(4,5)P2 regulator, Arf6, rescued the disrupted trafficking pathways in nrca14 cones. Our study describes a specific role for SynJ1 in autophagosomal and endosomal trafficking and provides evidence that PI(4,5)P2 participates in autophagy in a neuronal cell type. -/- . (shrink)

Members of the CAR group of Ig‐like type I transmembrane proteins mediate homotypic cell adhesion, share a common overall extracellular domain structure and are closely related at the amino acid sequence level. CAR proteins are often found at tight junctions and interact with intracellular scaffolding proteins, suggesting that they might modulate tight junction assembly or function. However, impairment of tight junction integrity has not been reported in mouse knockout models or zebrafish mutants of CAR members. In contrast, in the (...) same knockout models deficits in gap junction communication were detected in several organ systems, including the atrioventricular node of the heart, smooth muscle cells of the intestine and the ureter and in Sertoli cells of the testes. Possible interactions between BT‐IgSF and connexin41.8 on the disturbed pattern of pigment stripes found in zebrafish mutants and between ESAM and connexin43 during hematopoiesis in the mouse are also discussed. On the basis of the combined data and phenotypic similarities between CAR member mutants and connexin mutants I hypothesize that they primarily play a role in the organization of gap junction communication. Also see the video abstract here: https://youtu.be/i0yq2KhuDAE. (shrink)

Evidence from Drosophila and also vertebrates predicts that two different sets of instructions may determine the development of the rostral and caudal parts of the body. This implies different cellular and inductive processes during gastrulation, whose genetic requirements remain to be understood. To date, four genes encoding transcription factors expressed in the presumptive vertebrate head during gastrulation have been studied at the functional level: Lim‐1, Otx‐2, HNF‐3β and goosecoid. We discuss here the potential functions of these genes in the formation (...) of rostral head as compared to posterior head and trunk, and in the light of recent fate map and expression analyses in mouse, chick, Xenopus and zebrafish. These data indicate that Lim‐1, Otx‐2 and HNF‐3β may be involved in the same genetic pathway controlling the formation of the prechordal mesendoderm, which is subsequently required for rostral head development. goosecoid may act in a parallel pathway, possibly in conjunction with other, yet unidentified, factors. (shrink)

The establishment of a functional vascular system requires multiple complex steps throughout embryogenesis, from endothelial cell (EC) specification to vascular patterning into venous and arterial hierarchies. Following the initial assembly of ECs into a network of cord‐like structures, vascular expansion and remodeling occur rapidly through morphogenetic events including vessel sprouting, fusion, and pruning. In addition, vascular morphogenesis encompasses the process of lumen formation, critical for the transformation of cords into perfusable vascular tubes. Studies in mouse, zebrafish, frog, and human (...) endothelial cells have begun to outline the cellular and molecular requirements underlying lumen formation. Although the lumen can be generated through diverse mechanisms, the coordinated participation of multiple conserved molecules including transcription factors, small GTPases, and adhesion and polarity proteins remains a fundamental principle, leading us closer to a more thorough understanding of this complex event. (shrink)

Genetic analysis of Drosophila has shown that a morphogenetic gradient of the Transforming Growth Factor‐β family member dpp patterns the embryonic dorsalventral axis. Molecular and embryological evidence from Xenopus has strongly suggested a similar role for Bmp‐4, the dpp homolog, in patterning the dorsalventral axis of chordates. A recent report has now identified mutations in two genes, dino and swirl, that disrupt dorsal‐ventral patterning in the zebrafish Danio rerio(1). Characterization of these mutations parallels findings from Drosophila, thus establishing a (...) genetic framework for the analysis of dorsalventral patterning in a vertebrate. (shrink)

Certain species of fish have recently become important model systems in comparative genomics and in developmental biology, in certain instances because of their small genome sizes (e.g., in the pufferfish) and, in other cases, because of the opportunity they provide to combine an easily accessible and experimentally manipulable embryology with the power of genetic approaches (e.g., in the zebrafish). The resulting accumulation of genomic information indicates that, surprisingly, many gene families of fish consist of more members than in mammals. (...) Most modern fish, including the zebrafish and medakka, are diploid organisms; however, the greater number of genes in fish was possibly caused by additional ancient genome duplications which happened in the lineage leading to modern ray-finned fishes but not along the lineage leading to tetrapods. Since these two lineages shared their last common ancestor (in the Devonian about 360 million years ago) individual duplicated members of gene families were later lost in fish. Interestingly, comparative data indicate that, in some cases, genes in mammals even serve somewhat different functions than their homologues in fish, highlighting that the degree of evolutionary relatedness of genes is not always a reliable predictor of their evolutionary conservation and their similarity of function. Since fish are phenotypically probably not more complex than mammals, it is possible that evolution took alternative paths to the “economics of genomics” through alternative solutions to gene regulation. It is suggested that the more complex genomic architecture of fish permitted them to adapt and speciate quickly in response to changing selective regimes. BioEssays 20:511–515, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

Classical mutations at the mouse Brachyury (T) locus were discovered because they lead to shortened tails in heterozygous newborns. no tail (ntl) mutants in the zebrafish, as their name suggests, show a similar phenotype. In Drosophila, mutants in the brachyenteron (byn) gene disrupt hindgut formation. These genes all encode T-box proteins, a class of sequence-specific DNA binding proteins and transcription factors. Mutations in the C. elegans mab-9 gene cause massive defects in the male tail because of failed fate decisions (...) in two tail progenitor cells. In a recent paper, Woollard and Hodgkin1 have cloned the mab-9 gene and found that it too encodes a T-box protein, similar to Brachyury in vertebrates and brachyenteron in Drosophila. The authors suggest that their results support models for an evolutionarily ancient role for these genes in hindgut formation. We will discuss this proposal and try to decide whether the gene sequences, gene interactions and gene expression patterns allow any conclusions to be made about the rear end of the ancestral metazoan. BioEssays 22:781–785, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

After a vertebrate dies, many of its organ systems, tissues, and cells remain functional while its body no longer works as a whole. We define this state as the “twilight of death” − the transition from a living body to a decomposed corpse. We claim that the study of the twilight of death is important to ethical, legal and medical science. We examined gene expression at the twilight of death in the zebrafish and mouse reaching the conclusion that apparently (...) thousands of transcripts significantly increase in abundance from life to several hours/days postmortem relative to live controls. Transcript dynamics of different genes provided “proof-of-principle” that models accurately predict an individual's elapsed-time-of-death. While many transcripts were associated with survival and stress compensation, others were associated with epigenetic factors, developmental control, and cancer. Future studies are needed to determine whether the high incidence of cancer in transplant recipients is due to the postmortem processes in donor organs. In organismal death, some organ systems, tissues and cells remain functional while the body no longer works as a whole. In the “twilight of death” − the transition from a living body to a decomposed corpse − thousands of gene transcripts increase in abundance relative to live controls. (shrink)

The recent publication by Wylie et al. is reviewed, demonstrating that the p53 protein regulates the movement of transposons. While this work presents genetic evidence for a piRNA‐mediated p53 interaction with transposons in Drosophila and zebrafish, it is herein placed in the context of a decade or so of additional work that demonstrated a role for p53 in regulating transposons and other repetitive elements. The line of thought in those studies began with the observation that transposons damage DNA and (...) p53 regulates DNA damage. The presence of transposon movement can increase the rate of evolution in the germ line and alter genes involved in signal transduction pathways. Transposition can also play an important role in cancers where the p53 gene function is often mutated. This is particularly interesting as recent work has shown that de‐repression of repetitive elements in cancer has important consequences for the immune system and tumor microenvironment. (shrink)

On the basis of the evidence that tumor development is suppressed by the embryonic microenvironment, some experiments using the factors taken from Zebrafish embryo at precise stages of cell differentiation were made. These experiments demonstrated a significant growth inhibition on different tumor cell lines in vitro. The observed mechanism of tumor growth inhibition is connected with the key-role cell cycle regulation molecules, such as p53 and pRb, which are modified by transcriptional or post-translational processes. Research on apoptosis and differentiation (...) revealed that treatment with these factors induces caspase-3 with a p73 apoptotic-dependent pathway activation and a concurrent significant normalization of e-cadherin and beta-catenin ratio. Other experiments found a synergistic effect on the colon cancer proliferation curve after the concurrent treatment with these factors and 5-fluorouracil. Finally, a product prepared for human therapy demonstrated 19.8% regression and 16% stable disease in an... (shrink)

Experiments carried out on different tumor cell lines showed a significative growth reduction of all treated lines due to the administration of zebrafish embryo extracts withdrawn at different stem cells differentiation stages. Research conducted in order to establish which molecular events were involved in control and downregulation of cancer cell lines demonstrated a transcriptional regulation of the key cell cycle onco-supressor gene, like p53 and a post-translational modification of molecules, like pRb. Research on apoptosis and differentiation processes showed that (...) stem cells differentiating factors induce caspase-3 activation, mainly through E2F-1 gene regulation, thus hyper expressing c-Myc and activating a p73-dependent apoptotic pathway. Moreover, we demonstrated a concurrent and significative normalization of the e-cadherin/β-catenin expression, with an e-cadherin rise. Administration of SCDF in an open clinical randomized clinical trail conducted on 179 patients affected by interme... (shrink)

There is now a rapidly expanding population of interlinked developmental biology databases on the World Wide Web that can be readily accessed from a desk‐top PC using programs such as Netscape or Mosaic. These databases cover popular organisms (Arabidopsis, Caenorhabditis, Drosophila, zebrafish, mouse, etc.) and include gene and protein sequences, lists of mutants, information on resources and techniques, and teaching aids. More complex are databases relating domains of gene expression to embryonic anatomy and these range from existing text‐based systems (...) for specific organs such as kidney, to a massive project under development, that will cover gene expression during the whole of mouse embryogenesis. In this brief article, we review selected examples of databases currently available, look forward to what will be available soon, and explain how to gain access to the World Wide Web. (shrink)

Fezf1 and Fezf2 are highly conserved transcription factors that were first identified by their specific expression in the anterior neuroepithelium of Xenopus and zebrafish embryos. These proteins share an N‐terminal domain with homology to the canonical engrailed repressor motif and a C‐terminal DNA binding domain containing six C2H2 zinc‐finger repeats. Over a decade of study indicates that the Fez proteins play critical roles during nervous system development in species as diverse as fruit flies and mice. Herein we discuss recent (...) progress in understanding the functions of Fezf1 and Fezf2 in neurogenesis and cell fate specification during mammalian nervous system development. Going forward we believe that efforts should focus on understanding how expression of these factors is precisely regulated, and on identifying target DNA sequences and interacting partners. Such knowledge may reveal the mechanisms by which Fezf1 and Fezf2 accomplish both independent and redundant functions across diverse tissue and cell types. (shrink)

Variations in human skin pigmentation are obvious, but how have skin colour differences evolved? Although clearly a polymorphic trait, the number and identity of key variants has remained unclear. Investigation of pigmentation phenotypes in model organisms provides a route to identify these genes and showed MC1R to be one key locus. Now, cloning of a classic zebrafish mutant, golden, identifies slc24a5 as a gene involved in fish skin pigmentation.1 Strikingly this study identifies the human orthologue, SLC24A5, as likely to (...) make a major contribution to the pale skin colouration of Western Europeans. BioEssays 28: 578–582, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal of (...) transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis‐regulatory elements. BioEssays 24:564–572, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

First isolated in the fly and now characterised in vertebrates, the Slit proteins have emerged as pivotal components controlling the guidance of axonal growth cones and the directional migration of neuronal precursors. As well as extensive expression during development of the central nervous system (CNS), the Slit proteins exhibit a striking array of expression sites in non-neuronal tissues, including the urogenital system, limb primordia and developing eye. Zebrafish Slit has been shown to mediate mesodermal migration during gastrulation, while Drosophila (...) slit guides the migration of mesodermal cells during myogenesis. This suggests that the actions of these secreted molecules are not simply confined to the sphere of CNS development, but rather act in a more general fashion during development and throughout the lifetime of an organism. This review focuses on the non-neuronal activities of Slit proteins, highlighting a common role for the Slit family in cellular migration. (shrink)

Every cartilage and bone in the vertebrate skeleton has a precise shape and position. The head skeleton develops in the embryo from the neural crest, which emigrates from the neural ectoderm and forms the skull and pharyngeal arches. Recent genetic data from mice and zebrafish suggest that cells in the pharyngeal segments are specified by positional information in at least two dimensions, Hox genes along the anterior‐posterior axis and other homeobox genes along the dorsal‐ventral axis within a segment. Many (...) zebrafish and human mutant phenotypes indicate that additional genes are required for the development of groups of adjacent pharyngeal arches and for patterning along the mediolateral axis of the skull. The complementary genetic approaches in humans, mice and fish reveal networks of genes that specify the complex morphology of the head skeleton along a relatively simple set of coordinates. (shrink)

All cells have electric potentials across their membranes, but is there really compelling evidence to think that such potentials are used as instructional cues in developmental biology? Numerous reports indicate that, in fact, steady, weak bioelectric fields are observed throughout biology and function during diverse biological processes, including development. Bioelectric fields, generated upon amputation, are also likely to play a key role during vertebrate regeneration by providing the instructive cues needed to direct migrating cells to form a wound epithelium, a (...) structure unique to regenerating animals. However, mechanistic insight is still sorely lacking in the field. What are the genes required for bioelectric‐dependent cell migration during regeneration? The power of genetics combined with the use of zebrafish offers the best opportunity for unbiased identification of the molecular players in bioelectricity. BioEssays 29:1133–1137, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

While largely studied because of their harmful effects on human health, there is growing appreciation that bacteria are important partners for invertebrates and vertebrates, including man. Epithelia in metazoans do not only select their microbiota; a coevolved consortium of microbes enables both invertebrates and vertebrates to expand the range of diet supply, to shape the complex immune system and to control pathogenic bacteria. Microbes in zebrafish and mice regulate gut epithelial homeostasis. In a squid, microbes control the development of (...) the symbiotic light organ. These discoveries point to a key role for bacteria in any metazoan existence, and imply that beneficial bacteria‐host interactions should be considered an integral part of development and evolution. (shrink)

The multiplicity of deubiquitinating enzymes (DUBs) encoded by vertebrate genomes is partly attributable to whole genome duplication events that occurred early in chordate evolution. By surveying the literature for the largest family of DUBs (the ubiquitin-specific proteases), extensive functional redundancy for duplicated genes has been confirmed as opposed to singletons. Dramatically conflicting results have been reported for loss of function studies conducted through RNA interference as opposed to inactivating mutations, but the contradictory findings can be reconciled by a recently proposed (...) compensatory mechanism involving nonsense-mediated RNA degradation. Duplicated genes are often inactivated to become pseudogenes, and it is proposed that such is the fate of the USP15 gene of zebrafish, a commonly used model system. As it is reviewed here, these observations have implications not only for the interpretation of model system phenotypes but also for therapeutic interventions designed to target DUBs. (shrink)

Wnt proteins can activate different intracellular signaling cascades in various organisms by interacting with receptors of the Frizzled family. The first identified Wnt signaling pathway, the Wnt/β‐catenin pathway, has been studied in much detail and is highly conserved among species. As to non‐canonical Wnt pathways, the current situation is more nebulous partly because the intracellular mediators of this pathway are not yet fully understood and, in some cases, even identified. However, there are increasing data that prove the existence of non‐canonical (...) Wnt signaling and demonstrate its involvement in different developmental processes. In vertebrates, Wnt‐11 and Wnt‐5A can activate the Wnt/JNK pathway, which resembles the planar cell polarity pathway in Drosophila. The Wnt/Ca2+‐pathway has only been described in Xenopus and zebrafish so far and it is unclear whether it also exists in other organisms. Two recent papers provide us with new insight into non‐canonical Wnt signaling by (1) presenting a new intracellular mediator of non‐canonical signaling in Xenopus1 and (2) implicating the existence of an additional non‐canonical Wnt signaling pathway in flies.2 BioEssays 24:881–884, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Epithelial stem cells have been identified in integumental structures such as hairs and continuously growing teeth of various rodents, and in the gut. Here we propose the involvement of epithelial stem cells in the continuous tooth replacement that characterizes non‐mammalian vertebrates, as exemplified by the zebrafish. Arguments are based on morphological observations of tooth renewal in the zebrafish and on the similarities between molecular control of hair and tooth formation. Dissection of the molecular cascades underlying the regulation of (...) the epithelial stem cell niche might open perspectives for new regenerative treatment strategies in clinical dentistry. BioEssays 26:665–671, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Factors affecting transcriptional elongation have been characterized extensively in in vitro, single cell (yeast) and cell culture systems; however, data from the context of multicellular organisms has been relatively scarce. While studies in homogeneous cell populations have been highly informative about the underlying molecular mechanisms and prevalence of polymerase pausing, they do not reveal the biological impact of perturbing this regulation in an animal. The core components regulating pausing are expressed in all animal cells and are recruited to the majority (...) of genes, however, disrupting their function often results in discrete phenotypic effects. Mutations in genes encoding key regulators of transcriptional pausing have been recovered from several genetic screens for specific phenotypes or interactions with specific factors in mice, zebrafish and flies. Analysis of these mutations has revealed that control of transcriptional pausing is critical for a diverse range of biological pathways essential for animal development and survival. (shrink)

Hepatocellular carcinoma represents the third leading cause of cancer-related death. Because HCC is multicentric with time, excluding the few transplanted patients, sooner or later it becomes untreatable with loco-regional therapies and, until some years ago, it was not responsive to systemic therapies. In 2005 a randomized trial indicated the efficacy of a product containing stem cell differentiation stage factors taken from zebrafish embryos during the stage in which the totipotent stem cells are differentiating into the pluripotent adult stem cells. (...) In such a trial the patients, with “intermediate” and “advanced” HCC according to Barcelona Clinic Liver Cancer/American Association for the Study of Liver Diseases guidelines, presented benefit in terms of performance status and objective tumoral response, with some cases of complete response, that is, sustained disappearance of the neoplastic areas or blood supply therein, accompanied by normalization of alpha-fetoprotein... (shrink)

The cardiovascular system has the life‐providing task of delivering oxygen and any flaw in this system can be life‐threatening. This has encouraged extensive studies to elucidate the mechanisms behind cardiovascular development/homeostasis. The zebrafish has emerged as a formidable tool to speed up this quest, as illustrated in a recent issue of Nature Genetics.1 Baculovirus IAP repeat c2 (BIRC2), also termed cellular inhibitor of apoptosis (cIAP)‐1, was found to specifically prevent endothelial cells (ECs, lining the inside of vessels) from going (...) into suicide mode (‘apoptosis’) and so preserve vessel integrity. Here, we summarize the factors determining vascular integrity and elaborate on the suitability of the zebrafish to study this phenomenon. BioEssays 30:418–422, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The power of sexual selection to influence the evolution of morphological traits was first proposed more than 130 years ago by Darwin. Though long a controversial idea, it has been documented in recent decades for a host of animal species. Yet few of the established sexually selected features have been explored at the level of their genetic or molecular foundations. In a recent report, Zauner et al.1 describe some of the molecular features associated with one of the best characterized of (...) sexually selected traits, the male‐specific tail “sword” seen in certain species of the fish genus Xiphophorus. Zauner et al. find that the msxC gene, a gene previously implicated in fin development from work in zebrafish, is dramatically and specifically upregulated in the development of the ventral caudal fin rays, which give rise to the sword, in males. The results provide the first molecular insight into the development of this sexually selected trait while prompting new questions about the structure of the entire genetic network that underlies this trait. To fully understand the molecular‐genetic and evolutionary history of this network, however, it will be essential to determine whether sword‐development is a basal or derived trait in Xiphophorus. BioEssays 26:116–119, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

Fish farming is one of the fastest growing sectors of agriculture, attracting considerable attention to the question of whether existing farming regulations and animal welfare laws are adequate to deal with the expanding role of fish in feeding humans. The role of fish as model organisms in scientific research is also expanding -- a majority of research biology departments now keep zebrafish for the purposes of genome biology, and they are used widely used for basic neuroscience research. However, due (...) to their diversity and distance from mammalian biology, fish pose difficult questions for the application of legal and ethical principles of animal welfare. This paper reviews the developing legal and scientific context in which such questions must be answered. (shrink)

Many apparently complex mechanisms in biology, especially in embryology and molecular biology, can be explained easily by reasoning at the level of the “efficient cause” of the observed phenomenology: the mechanism can then be explained by a simple geometrical argument or a variational principle, leading to the solution of an optimization problem, for example, via the co-existence of a minimization and a maximization problem . Passing from a microscopic level to the macroscopic level often involves an averaging effect that gives (...) birth to a global functional feature . We will illustrate these general principles by building in four different domains of application “a minima” models and showing the main properties of their solutions: extraction of a minimal RNA structure functioning as the first “peptidic machine,” a kind of ancestral ribosome; study of a genetic regulatory network of Drosophila centred on Engrailed gene and expressing successively two genes inside a limit cycle; study of a genetic network regulating neural activity and proliferation in mammals; and study of a simple geometric model of epiboly in zebrafish. (shrink)

In spite of the importance of point mutations for evolution and human diseases, their natural spectrum of incidence in different species is not known. Here I propose to determine these spectra by comparing consecutive sequence periods in stretches of repetitive DNA. The article presents the analysis of more than 51,000 such point mutations identified by this approach in the genomes of human, chimpanzee, rat, mouse, pufferfish, zebrafish, and sea squirt. I propose to explain the observed spectra by auto‐mutagenic mechanisms (...) of genome variation involving the inter‐conversions of nucleotides, single base‐pair inversions and their combinations. (shrink)