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PubMed2006

A golden clue to human skin colour variation.

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.

Animals↗

PubMed2003

Shaping the zebrafish notochord.

Promptly after the notochord domain is specified in the vertebrate dorsal mesoderm, it undergoes dramatic morphogenesis. Beginning during gastrulation, convergence and extension movements change a squat cellular array into a narrow, elongated one that defines the primary axis of the embryo. Convergence and extension might be coupled by a highly organized cellular intermixing known as mediolateral intercalation behavior (MIB). To learn whether MIB drives early morphogenesis of the zebrafish notochord, we made 4D recordings and quantitatively analyzed both local cellular interactions and global changes in the shape of the dorsal mesodermal field. We show that MIB appears to mediate convergence and can account for extension throughout the dorsal mesoderm. Comparing the notochord and adjacent somitic mesoderm reveals that extension can be regulated separately from convergence. Moreover, mutational analysis shows that extension does not require convergence. Hence, a cellular machine separate from MIB that can drive dorsal mesodermal extension exists in the zebrafish gastrula. The likely redundant control of morphogenesis may provide for plasticity at this critical stage of early development.

Animals↗

PubMed2004

Induction of reversible hemolytic anemia in living zebrafish using a novel small molecule.

We used zebrafish to screen and identify small molecules that affect the process of vertebrate hematopoietic development. Zebrafish embryos were exposed to a library of 5000 synthetic compounds and screened for defects in primitive erythropoiesis. Here, we present the characterization of hemolytic anemia induced in zebrafish by the small molecule 5115318 (3-[5-methyl-furan 2-yl]-propionic acid N'-phenyl-hydrazide). This compound is capable of generating hemoglobin aggregates and Heinz bodies in red cells in vivo only. The induced anemia is reversible and treated fish recover in about 4 days. This study shows the feasibility of using zebrafish to screen for small molecules that can modulate the specific process of erythropoiesis.

Anemia, Hemolytic↗

PubMed2026

Environmental benzene exposure induces a conserved neutrophil degranulation program across species.

Immune systems have evolved under constant pressure from pathogens and environmental challenges, leading to the emergence of conserved defense mechanisms across diverse organisms. Evidence indicates that environmental exposures perturb immune regulatory networks, particularly during development, when transcriptional programs governing hematopoiesis, immune cell differentiation, and inflammatory signaling are highly dynamic and sensitive to external stressors. Volatile organic compounds represent an important but incompletely understood source of immunological perturbation. Among these, benzene is a ubiquitous environmental contaminant associated with hematotoxicity and immune dysregulation; however, transcriptional responses to environmentally relevant low-level exposures during development remain poorly characterized. To determine whether benzene exposure engages conserved cross-species immune regulatory pathways, we performed a comparative transcriptomic analysis integrating developmental tissues from 3 vertebrate systems: human placenta, murine placenta, and zebrafish larvae. Bulk RNA sequencing datasets were analyzed to identify transcriptional responses associated with benzene exposure in experimental models (≤5 ppm) and with benzene adduct levels in maternal plasma for human samples. Because placental gene expression exhibits strong sexual dimorphism, murine datasets were stratified by fetal sex. Pathway- and network-level analyses were used to identify conserved biological responses. We observed a striking convergence on activation of innate immune pathways associated with neutrophil degranulation, IL-8 signaling, and Rho GTPase-mediated inflammatory responses. Further, network analyses identified CXCL8 and ERK1/2 as shared regulatory hubs linking transcriptional responses across datasets. Together, these findings uncover an evolutionarily conserved innate immune signature associated with benzene exposure during vertebrate development, suggesting that environmental chemical perturbations may disrupt fundamental immune regulatory programs across species.

Animals↗

PubMed2005

Intestinal growth and differentiation in zebrafish.

Intestinal development in amniotes is driven by interactions between progenitor cells derived from the three primary germ layers. Genetic analyses and gene targeting experiments in zebrafish offer a novel approach to dissect such interactions at a molecular level. Here we show that intestinal anatomy and architecture in zebrafish closely resembles the anatomy and architecture of the mammalian small intestine. The zebrafish intestine is regionalized and the various segments can be identified by epithelial markers whose expression is already segregated at the onset of intestinal differentiation. Differentiation of cells derived from the three primary germ layers begins more or less contemporaneously, and is preceded by a stage in which there is rapid cell proliferation and maturation of epithelial cell polarization. Analysis of zebrafish mutants with altered epithelial survival reveals that seemingly related single gene defects have different effects on epithelial differentiation and smooth muscle and enteric nervous system development.

Animals↗

PubMedDate not supplied

Comprehensive analysis of blood coagulation pathways in teleostei: evolution of coagulation factor genes and identification of zebrafish factor VIIi.

It is not clear how the complex mammalian coagulation pathways evolved from an entirely dissimilar invertebrate coagulation cascade. Comprehensive analysis of pro-coagulant factors and their regulators is lacking in early vertebrates to discern the mechanism of evolution of these genes from the invertebrates. To elucidate the coagulation pathways found in early vertebrates, zebrafish cDNAs/gene orthologues for major coagulant, anticoagulant, and fibrinolytic proteins were identified and characterized by homology to mammalian sequences. We found that zebrafish carry all hemostatic genes present in mammals, providing evidence that the coagulation system of teleosts is nearly identical to mammals. Zebrafish factor VII and X genes were identified and analyzed to reveal a novel factor VII-like gene flanked by the factor VII and factor X genes. This gene encodes a protein homologous to factor VII, but lacks critical residues for factor VII activity. Expression of the factor VII-like protein (named factor VIIi) demonstrated that it functions as an inhibitor of blood coagulation in biochemical assays using zebrafish or human plasmas. Analysis of intergenic DNA between the zebrafish VII/VIIi/X gene cluster and a Drosophila trypsin gene cluster revealed significant homology, and based upon these data, we propose a model for a rapid evolution of coagulation factors from the invertebrates.

Amino Acid Sequence↗

PubMed1999

Development of motor behaviour.

The development of motor behaviour depends on the differentiation of underlying circuitry. Recent work with the zebrafish brings the simple swimming behaviour of lower vertebrates and their embryos into focus as a suitable model to study the development of motor circuitry and its genetic control. Changes in connectivity and excitability contribute to the development of swimming in this simple system. In the chick embryo, limb motor circuitry is spontaneously active before motor axons reach their muscle targets, and it has properties in common with the spontaneously active networks in the retina. The early rhythmic activity responsible for embryonic movement is probably a generalised property of developing spinal networks that precedes, and may be required for, the completion of functional locomotor circuitry.

Aging↗

PubMed2004

A direct role for Fgf but not Wnt in otic placode induction.

Induction of the otic placode, which gives rise to all tissues comprising the inner ear, is a fundamental aspect of vertebrate development. A number of studies indicate that fibroblast growth factor (Fgf), especially Fgf3, is necessary and sufficient for otic induction. However, an alternative model proposes that Fgf must cooperate with Wnt8 to induce otic differentiation. Using a genetic approach in zebrafish, we tested the roles of Fgf3, Fgf8 and Wnt8. We demonstrate that localized misexpression of either Fgf3 or Fgf8 is sufficient to induce ectopic otic placodes and vesicles, even in embryos lacking Wnt8. Wnt8 is expressed in the hindbrain around the time of otic induction, but loss of Wnt8 merely delays expression of preotic markers and otic vesicles form eventually. The delay in otic induction correlates closely with delayed expression of fgf3 and fgf8 in the hindbrain. Localized misexpression of Wnt8 is insufficient to induce ectopic otic tissue. By contrast, global misexpression of Wnt8 causes development of supernumerary placodes/vesicles, but this reflects posteriorization of the neural plate and consequent expansion of the hindbrain expression domains of Fgf3 and Fgf8. Embryos that misexpress Wnt8 globally but are depleted for Fgf3 and Fgf8 produce no otic tissue. Finally, cells in the preotic ectoderm express Fgf (but not Wnt) reporter genes. Thus, preotic cells respond directly to Fgf but not Wnt8. We propose that Wnt8 serves to regulate timely expression of Fgf3 and Fgf8 in the hindbrain, and that Fgf from the hindbrain then acts directly on preplacodal cells to induce otic differentiation.

Animals↗

PubMed2002

The limb identity gene Tbx5 promotes limb initiation by interacting with Wnt2b and Fgf10.

A major gap in our knowledge of development is how the growth and identity of tissues and organs are linked during embryogenesis. The vertebrate limb is one of the best models to study these processes. Combining mutant analyses with gain- and loss-of-function approaches in zebrafish and chick embryos, we show that Tbx5, in addition to its role governing forelimb identity, is both necessary and sufficient for limb outgrowth. We find that Tbx5 functions downstream of WNT signaling to regulate Fgf10, which, in turn, maintains Tbx5 expression during limb outgrowth. Furthermore, our results indicate that Tbx5 and Wnt2b function together to initiate and specify forelimb outgrowth and identity. The molecular interactions governed by members of the T-box, Wnt and Fgf gene families uncovered in this study provide a framework for understanding not only limb development, but how outgrowth and identity of other tissues and organs of the embryo may be regulated.

Amino Acid Sequence↗

PubMed2000

Zebrafish on the move: towards a behavior-genetic analysis of vertebrate vision.

Behavioral screens have uncovered dozens of zebrafish mutants with striking visual defects. In parallel with mutant studies, recent psychophysical experiments indicate that zebrafish are capable of high-level motion processing, previously thought to be restricted to animals with a visual cortex. It should be possible now to devise assays to screen for mutations in visual perception.

Animals↗

PubMed2000

Double-stranded RNA injection produces null phenotypes in zebrafish.

Zebrafish is a simple vertebrate that has many attributes that make it ideal for the study of developmental genetics. One feature that has been lacking in this model system is the ability to disable specifically targeted genes. Recently, double-stranded RNA has been used to silence gene expression in the nematode Caenorhabditis elegans. We have found that expression of the green fluorescent protein (GFP) from a microinjected plasmid vector can be suppressed in zebrafish embryos by the coinjection of a double-stranded RNA that is specifically targeted to GFP. To determine that double-stranded RNA can attenuate endogenous gene expression, single-cell zebrafish embryos were injected with double-stranded RNA specifically targeted to Zf-T and Pax6.1. We found that microinjection of double-stranded Zf-T RNA resulted in a high incidence of a phenotype similar to that of ntl. Furthermore, Zf-T gene expression could not be detected by in situ hybridization and the message was decreased by 75% by semiquantitative RT-PCR in 12-h embryos that had been injected with the double-stranded RNA. Expression of the zebrafish genes sonic hedgehog and floating head was altered in the embryos microinjected with the Zf-T double-stranded RNA in a manner that is remarkably similar to the zebrafish no-tail mutant. Microinjection of double-stranded RNA targeted to Pax6.1 was associated with depressed expression of Pax6. 1 and resulted in absent or greatly reduced eye and forebrain development, similar to the phenotype seen in mouse mutants. Simultaneous injection of Pax6.1 and Zf-T resulted in embryos lacking notochords, eyes, and brain structures.

Animals↗

PubMed1999

Restricted expression of cardiac myosin genes reveals regulated aspects of heart tube assembly in zebrafish.

The embryonic vertebrate heart is divided into two major chambers, an anterior ventricle and a posterior atrium. Although the fundamental differences between ventricular and atrial tissues are well documented, it is not known when and how cardiac anterior-posterior (A-P) patterning occurs. The expression patterns of two zebrafish cardiac myosin genes, cardiac myosin light chain 2 (cmlc2) and ventricular myosin heavy chain (vmhc), allow us to distinguish two populations of myocardial precursors at an early stage, well before the heart tube forms. These myocardial subpopulations, which may represent the ventricular and atrial precursors, are organized in a medial-lateral pattern within the precardiac mesoderm. Our examinations of cmlc2 and vmhc expression throughout the process of heart tube assembly indicate the important role of an intermediate structure, the cardiac cone, in the conversion of this early medial-lateral pattern into the A-P pattern of the heart tube. To gain insight into the genetic regulation of heart tube assembly and patterning, we examine cmlc2 and vmhc expression in several zebrafish mutants. Analyses of mutations that cause cardia bifida demonstrate that the achievement of a proper cardiac A-P pattern does not depend upon cardiac fusion. On the other hand, cardiac fusion does not ensure the proper A-P orientation of the ventricle and atrium, as demonstrated by the heart and soul mutation, which blocks cardiac cone morphogenesis. Finally, the pandora mutation interferes with the establishment of the early medial-lateral myocardial pattern. Altogether, these data suggest new models for the mechanisms that regulate the formation of a patterned heart tube and provide an important framework for future analyses of zebrafish mutants with defects in this process.

Animals↗

PubMed2000

Binding properties of three neuropeptide Y receptor subtypes from zebrafish: comparison with mammalian Y1 receptors.

Neuropeptide Y (NPY) and peptide YY (PYY) are two related 36-amino-acid peptides found in all vertebrates and are involved in many physiological processes. Five receptor subtypes have been cloned in mammals (Y1, Y2, Y4, Y5, and y6). We have recently cloned three NPY/PYY receptor subtypes in zebrafish, called Ya, Yb, and Yc. Here we report on a direct comparison of the pharmacological properties of these three receptors in vitro using porcine NPY with alanine substitutions in positions 33-36 as ligands and three analogues with internal deletions: [Ahx(8-20)]NPY, [Ahx(8-20), Pro(34)]NPY, and [Ahx(5-24)]NPY. In all cases, the zYc receptor was the most sensitive to the modifications of the NPY molecule and zYa was the least sensitive (except for the Arg --> Ala replacement at position 33). Our data identified zYa as a receptor that can bind ligands specific for Y1, Y2, and Y4 receptors, while zYb and zYc were more Y1-like. All peptides with internal deletions bound to the zYa receptor with affinities similar to that of intact pNPY. Neither the Y1-selective antagonists BIBP3226 and SR120819A nor the Y2-selective BIIE0246 bound to any of the zebrafish receptors, although the amino acids identified as important for BIBP3226 binding were almost completely conserved. These results may prove helpful in molecular modeling of the three-dimensional receptor structure.

Amino Acid Sequence↗

PubMed2002

Specification of zebrafish neural crest.

Analysis of neural crest cells in wild-type zebrafish and in isolated mutants has complemented studies in other organisms and has led to a greater understanding of the processes of cell fate and regional specification. Analysis of pigment cell development suggests that neural crest cell fate specification results from a combination of intrinsic cues such as differential expression of transcription factors and external factors such as the Wnts. Whether this model can be generalized to accommodate other neural crest cell fates remains an active area of research. Regional specification of neural crest appears to be coordinated by similar combinations of internal factors such as the hox genes, and extrinsic cues such as retinoic acid and endothelins. There is still a wealth of zebrafish mutations whose molecular bases remain unknown, and it is likely that the revelation of the underlying genes will both broaden and alter our understanding of specification within the neural crest.

Animals↗

PubMed2005

Model for the distributions of k-mers in DNA sequences.

The evolutionary features based on the distributions of k-mers in the DNA sequences of various organisms are studied. The organisms are classified into three groups based on their evolutionary periods: (a) E. coli and T. pallidum (b) yeast, zebrafish, A. thaliana, and fruit fly, (c) mouse, chicken, and human. The distributions of 6-mers of these three groups are shown to be, respectively, (a) unimodal, (b) unimodal with peaks generally shifted to smaller frequencies of occurrence, (c) bimodal. To describe the bimodal feature of the k-mer distributions of group (c), a model based on the cytosine-guanine " CG" content of the DNA sequences is introduced and shown to provide reasonably good agreements.

Animals↗

PubMed1995

Developmental patterning of rod and cone photoreceptors in embryonic zebrafish.

Cone photoreceptors in the zebrafish retina are arranged in a crystalline lattice, with each spectral subtype at a specific position in the array; rod photoreceptors are inserted around the cones. Patterning events and developmental mechanisms that lead to the formation of the cone mosaic are not known. To begin investigating this issue, we examined the initial stages of opsin expression in zebrafish embryos by in situ hybridization with goldfish opsin cRNA probes to determine how and when the cone mosaic pattern arises. We found both differences and similarities in the spatiotemporal patterns of rod and cone development, which suggest the following: 1) Expression of opsin message (including rod opsin, blue and red cone opsins) was found in a ventral patch of retina located nasal to the choroid fissure. 2) The cone mosaic pattern was generated by a crystallization-like process initiated in the precocial ventral patch and secondarily in nasal retina, which then swept like a wave into dorsotemporal retina. 3) The remainder of the retina, suggesting that these precocial rods might differ from typical rods. 4) Developmental maturation of rods in zebrafish, as reflected by expression of opsin, may be accelerated compared to cones, which are thought to become postmitotic before rods. These data are consistent with a model in which lateral inductive interactions among differentiating photoreceptors lead to patterning of the array.

Animals↗

PubMed2003

Evidence for developmental linkage of pigment patterns with body size and shape in danios (Teleostei: Cyprinidae).

Variation in pigment patterns in fishes is known to be subject to natural and sexual selection, but the mechanisms by which that variation is generated are only beginning to be understood. Theoretical models of pigment pattern formation in animals suggest that the size and shape of the organism at the time of pattern determination as well as subsequent growth time are important determinants of pattern. However, few data document the empirical relationship of pigment patterning with size, shape, and growth. Here we document patterns of growth in relation to pigment pattern formation in the zebrafish (Danio rerio) and six close relatives. In all species examined, establishment of adult pigment pattern within a particular region of the body is associated with a period of substantial growth and shape change in that region of the body. Furthermore, forms with more horizontal stripes on the midbody as adults (Danio rerio and D. rerio "leo") are larger at the time pigment cells begin to assume their adult pattern. Finally, continued deepening of the body as the pigment pattern develops is associated with vertical distortions and reticulations in the patterns of D. malabaricus and D. browni. These results are consistent with the predictions of theoretical models that size, growth, and shape change are critical determinants of pigment patterning, and suggest that variation in pigment pattern may arise in part through differential allometric growth between species.

Analysis of Variance↗

PubMed2005

Medial floor plate formation in zebrafish consists of two phases and requires trunk-derived Midkine-a.

The medial floor plate (MFP) organizes the specification of neurons and outgrowth of axons in the ventral spinal cord of vertebrates. We show that the growth factor Midkine-a, expressed in the paraxial mesoderm, is required for formation of the MFP in zebrafish. Our epistatic analyses demonstrate that development of MFP comprises two independent sequential phases. Following initial MFP induction in the gastrula organizer, Midkine-a regulates allocation of MFP cells during subsequent development. Thus in zebrafish, trunk-derived signals are required for complete MFP formation from a common pool of organizer-derived midline precursor cells.

Animals↗