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PubMed1997

Genetic dissection of vertebrate processes in the zebrafish: a comparison of uniparental and two-generation screens.

Genetic dissection is used to identify important genes in biological processes and is accomplished through the generation and study of mutations in model organisms. In diploid organisms, recessive mutations must be rendered hemizygous or homozygous for the mutant phenotype to be detected. In zebrafish (Danio rerio), this can be accomplished in two ways: (i) crosses between siblings who are potential carriers (in two-generation screens) and (ii) the generation of uniparental progeny. Two-generation screens have been the most productive to date but require substantial resources. However, uniparental screens involving haploids and half-tetrads (products of meiosis I) have also been productive, and require more modest resources. In genetic screens, the fraction of an average genome that is heterozygous (heterozygosity index) is inversely proportional to the likelihood that separate recessive mutations will be homozygous at the same time. Heterozygosity indices for haploid, half-tetrad, and two-generation screens are 0, 66, and 87.5%, respectively. Family sizes required to minimize bias in half-tetrad screens are also calculated. We conclude that gynogenetic half-tetrad screens are genetically robust and technically accessible to the independent researcher. The increasingly powerful genetic and experimental tools available for work with zebrafish can be used to address a broad range of questions in vertebrate biology.

Animals↗
PubMed2006

Functional characterization of visual opsin repertoire in Medaka (Oryzias latipes).

A variety of visual pigment repertoires present in fish species is believed due to the great variation under the water of light environment. A complete set of visual opsin genes has been isolated and characterized for absorption spectra and expression in the retina only in zebrafish. Medaka (Oryzias latipes) is a fish species phylogenetically distant from zebrafish and has served as an important vertebrate model system in molecular and developmental genetics. We previously isolated a medaka rod opsin gene (RH1). In the present study we isolated all the cone opsin genes of medaka by genome screening of a lambda-phage and bacterial artificial chromosome (BAC) libraries. The medaka genome contains two red, LWS-A and LWS-B, three green, RH2-A, RH2-B and RH2-C, and two blue, SWS2-A and SWS2-B, subtype opsin genes as well as a single-copy of the ultraviolet, SWS1, opsin gene. Previously only one gene was believed present for each opsin type as reported in a cDNA-based study. These subtype opsin genes are closely linked and must be the products of local gene duplications but not of a genome-wide duplication. Peak absorption spectra (lambda(max)) of the reconstituted photopigments with 11-cis retinal varied greatly among the three green opsins, 452 nm for RH2-A, 516 nm for RH2-B and 492 nm for RH2-C, and between the two blue opsins, 439 nm for SWS2-A and 405 nm for SWS2-B. Zebrafish also has multiple opsin subtypes, but phylogenetic analysis revealed that medaka and zebrafish gained the subtype opsins independently. The lambda and BAC DNA clones isolated in this study could be useful for investigating the regulatory mechanisms and evolutionary diversity of fish opsin genes.

Animals↗
PubMed2006

Zebrafish as a "biosensor"? Effects of ionizing radiation and amifostine on embryonic viability and development.

The zebrafish (Danio rerio) has emerged as a popular vertebrate model system for cancer and treatment-related research. Benefits include ease of care, rapid development, optical clarity of embryos, which allows visualization of major organ systems, and opportunities for genetic manipulation. However, specific parameters of radiation sensitivity have not been systematically documented. We investigated the effects of radiation and a radiomodifier on zebrafish viability and embryonic development. Embryos were exposed to gamma-radiation (5, 10, or 20 Gy) at sequential times postfertilization and serially assessed for viability and morphologic abnormalities. As expected, lethality and morphologic perturbations were more pronounced earlier in embryogenesis and with higher radiation doses and were partially reversed by amifostine. The effects of radiation and concurrent treatment with amifostine on the developmental organization of the eye and brain were striking. Radiation resulted in hypocellularity and disorganization of the cellular layers of the retina, effects partially reversed by amifostine, as well as lens opacification. Radiation strikingly reduced the volume of brain, but the volume loss was substantially blocked by amifostine. Increased terminal deoxyribonucleotidyl transferase-mediated dUTP nick end labeling signal was noted in both the irradiated eye and brain, but reduced by amifostine. Finally, irradiating embryos resulted in caspase activation detectable in 96-well microplates, which was proportional to the number of embryos and radiation dose; the degree of activation was markedly reduced by amifostine. These results together suggest the power and versatility of the zebrafish in assessing the effects of radiation and radiomodifiers on organ and tissue development.

Amifostine↗
PubMed1999

Preservation of duplicate genes by complementary, degenerative mutations.

The origin of organismal complexity is generally thought to be tightly coupled to the evolution of new gene functions arising subsequent to gene duplication. Under the classical model for the evolution of duplicate genes, one member of the duplicated pair usually degenerates within a few million years by accumulating deleterious mutations, while the other duplicate retains the original function. This model further predicts that on rare occasions, one duplicate may acquire a new adaptive function, resulting in the preservation of both members of the pair, one with the new function and the other retaining the old. However, empirical data suggest that a much greater proportion of gene duplicates is preserved than predicted by the classical model. Here we present a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum. Focusing on the regulatory complexity of eukaryotic genes, we show how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions. The duplication-degeneration-complementation (DDC) model predicts that (1) degenerative mutations in regulatory elements can increase rather than reduce the probability of duplicate gene preservation and (2) the usual mechanism of duplicate gene preservation is the partitioning of ancestral functions rather than the evolution of new functions. We present several examples (including analysis of a new engrailed gene in zebrafish) that appear to be consistent with the DDC model, and we suggest several analytical and experimental approaches for determining whether the complementary loss of gene subfunctions or the acquisition of novel functions are likely to be the primary mechanisms for the preservation of gene duplicates. For a newly duplicated paralog, survival depends on the outcome of the race between entropic decay and chance acquisition of an advantageous regulatory mutation. Sidow 1996(p. 717) On one hand, it may fix an advantageous allele giving it a slightly different, and selectable, function from its original copy. This initial fixation provides substantial protection against future fixation of null mutations, allowing additional mutations to accumulate that refine functional differentiation. Alternatively, a duplicate locus can instead first fix a null allele, becoming a pseudogene. Walsh 1995 (p. 426) Duplicated genes persist only if mutations create new and essential protein functions, an event that is predicted to occur rarely. Nadeau and Sankoff 1997 (p. 1259) Thus overall, with complex metazoans, the major mechanism for retention of ancient gene duplicates would appear to have been the acquisition of novel expression sites for developmental genes, with its accompanying opportunity for new gene roles underlying the progressive extension of development itself. Cooke et al. 1997 (p. 362)

Animals↗
PubMed2003

Saltatory control of isometric growth in the zebrafish caudal fin is disrupted in long fin and rapunzel mutants.

Zebrafish fins grow by sequentially adding new segments of bone to the distal end of each fin ray. In wild type zebrafish, segment addition is regulated such that an isometric relationship is maintained between fin length and body length over the lifespan of the growing fish. Using a novel, surrogate marker for fin growth in conjunction with cell proliferation assays, we demonstrate here that segment addition is not continuous, but rather proceeds by saltation. Saltation is a fundamental growth mechanism shared by disparate vertebrates, including humans. We further demonstrate that segment addition proceeds in conjunction with cyclic bursts of cell proliferation in the distal fin ray mesenchyme. In contrast, cells in the distal fin epidermis proliferate at a constant rate throughout the fin ray growth cycle. Finally, we show that two separate fin overgrowth mutants, long fin and rapunzel, bypass the stasis phase of the fin ray growth cycle to develop asymmetrical and symmetrical fin overgrowth, respectively.

Aging↗
PubMed2005

Transition from non-motile behaviour to directed migration during early PGC development in zebrafish.

The migration of zebrafish primordial germ cells (PGCs) is directed by SDF-1a and serves as a model for long-range chemokine-guided cell migration. Whereas the development and migration of zebrafish PGCs have been studied in great detail starting at mid-gastrulation stages when the cells exhibit guided active migration [7-8 hours post fertilization (hpf)], earlier stages have not yet been examined. Here we show that the PGCs acquire competence to respond to the chemokine following discrete maturation steps. Using the promoter of the novel gene askopos and RNA elements of nanos1 to drive GFP expression in PGCs, we found that immediately after their specification (about 3 hpf) PGCs exhibit simple cell shape. This stage is followed by a phase at which the cells assume complex morphology yet they neither change their position nor do they respond to SDF-1a. During the third phase, a transition into a ;migratory stage' occurs as PGCs become responsive to directional cues provided by somatic cells secreting the chemokine SDF-1a. This transition depends on zygotic transcription and on the function of the RNA-binding protein Dead end and is correlated with down regulation of the cell adhesion molecule E-cadherin. These distinctive morphological and molecular alterations could represent a general occurrence in similar processes critical for development and disease.

Animals↗
PubMed2006

Fgf16 is essential for pectoral fin bud formation in zebrafish.

Zebrafish pectoral fin bud formation is an excellent model for studying morphogenesis. Fibroblast growth factors (Fgfs) and sonic hedgehog (shh) are essential for pectoral fin bud formation. We found that Fgf16 was expressed in the apical ectodermal ridge (AER) of fin buds. A knockdown of Fgf16 function resulted in no fin bud outgrowth. Fgf16 is required for cell proliferation and differentiation in the mesenchyme and the AER of the fin buds, respectively. Fgf16 functions downstream of Fgf10, a mesenchymal factor, signaling to induce the expression of Fgf4 and Fgf8 in the AER. Fgf16 in the AER and shh in the zone of polarizing activity (ZPA) interact to induce and/or maintain each other's expression. These findings have revealed that Fgf16, a newly identified AER factor, plays a crucial role in pectoral fin bud outgrowth by mediating the interactions of AER-mesenchyme and AER-ZPA.

Animals↗
PubMed2005

Generation of segment polarity in the paraxial mesoderm of the zebrafish through a T-box-dependent inductive event.

The first morphological sign of vertebrate postcranial body segmentation is the sequential production from posterior paraxial mesoderm of blocks of cells termed somites. Each of these embryonic structures is polarized along the anterior/posterior axis, a subdivision first distinguished by marker gene expression restricted to rostral or caudal territories of forming somites. To better understand the generation of segment polarity in vertebrates, we have studied the zebrafish mutant fused somites (fss), because its paraxial mesoderm lacks segment polarity. Previously examined markers of caudal half-segment identity are widely expressed, whereas markers of rostral identity are either missing or dramatically down-regulated, suggesting that the paraxial mesoderm of the fss mutant embryo is profoundly caudalized. These findings gave rise to a model for the formation of segment polarity in the zebrafish in which caudal is the default identity for paraxial mesoderm, upon which is patterned rostral identity in an fss-dependent manner. In contrast to this scheme, the caudal marker gene ephrinA1 was recently shown to be down-regulated in fss embryos. We now show that notch5, another caudal identity marker and a component of the Delta/Notch signaling system, is not expressed in the paraxial mesoderm of early segmentation stage fss embryos. We use cell transplantation to create genetic mosaics between fss and wild-type embryos in order to assay the requirement for fss function in notch5 expression. In contrast to the expression of rostral markers, which have a cell-autonomous requirement for fss, expression of notch5 is induced in fss cells at short range by nearby wild-type cells, indicating a cell-non-autonomous requirement for fss function in this process. These new data suggest that segment polarity is created in a three-step process in which cells that have assumed a rostral identity must subsequently communicate with their partially caudalized neighbors in order to induce the fully caudalized state.

Animals↗
PubMed2006

Development of a new rapid measurement technique for fish embryo membrane permeability studies using impedance spectroscopy.

Information on fish embryo membrane permeability is vital in their cryopreservation. Whilst conventional volumetric measurement based assessment methods have been widely used in fish embryo membrane permeability studies, they are lengthy and reduce the capacity for multi-embryo measurement during an experimental run. A new rapid 'real-time' measurement technique is required to determine membrane permeability during cryoprotectant treatment. In this study, zebrafish (Danio rerio) embryo membrane permeability to cryoprotectants was investigated using impedance spectroscopy. An embryo holding cell, capable of holding up to 10 zebrafish embryos was built incorporating the original system electrods for measuring the impedance spectra. The holding cell was tested with deionised water and a series of KCl solutions with known conductance values to confirm the performance of the modified system. Untreated intact embryos were then tested to optimise the loading capacity and sensitivity of the system. To study the impedance changes of zebrafish embryos during cryoprotectant exposure, three, six or nine embryos at 50% epiboly stage were loaded into the holding cell in egg water, which was then removed and replaced by 0.5, 1.0, 2.0 or 3M methanol or dimethyl sulfoxide (DMSO). The impedance changes of the loaded embryos in different cryoprotectant solutions were monitored over 30 min at 22 degrees C, immediately following embryo exposure to cryoprotectants, at the frequency range of 10-10(6)Hz. The impedance changes of the embryos in egg water were used as controls. Results from this study showed that the optimum embryo loading level was six embryos per cell for each experimental run. The optimum frequency was identified at 10(3.14) or 1,380 Hz which provided good sensitivity and reproducibility. Significant impedance changes were detected after embryos were exposed to different concentrations of cryoprotectants. The results agreed well with those obtained from conventional volumetric based studies.

Animals↗
PubMed1995

Cell mixing during early epiboly in the zebrafish embryo.

Descendants of early blastomeres in the zebrafish come to populate distinctive regions of the fate map. We present a model suggesting that the distribution of cells in the early gastrula (the fate map stage) results from the passive response of cells to reproducible forces that change the overall shape of the blastoderm just prior to gastrulation. We suggest that one of the morphogenetic changes that accompanies epiboly, the upward doming of the yolk cell into the overlying blastoderm, could be responsible for cell mixing. In support of the model, we show that the timing, extent, and directions of cell mixing in the embryo accurately reflect the expectations of the model. Finally, we show that one portion of the gastrula, a marginal region that later gives rise to many of the mesendodermal derivatives, experiences little cell mixing during the doming process. As a result, this region in the gastrula is populated by the descendants of the subset of the early blastomeres that were originally at the margin. The finding that cytoplasm initially at the edge of the 1-celled blastodisc is transmitted specifically to mesendodermal precursors at the fate map stage raises the possibility that maternal determinants may contribute to initiation of embryonic patterning in the zebrafish embryo.

Animals↗
PubMed1994

Early neurogenesis in the zebrafish embryo.

Zebrafish embryos represent an attractive system for the study of early vertebrate neurogenesis. The embryos develop outside of the mother and are transparent allowing analysis at the cellular level in the living embryo during all phases of early neurogenesis. The teleostean neural tube is generated by a mechanism different from that of other vertebrates. A massive keel is formed first and the central canal appears by subsequent cavitation. Despite this, however, the organization of the neural plate and the neural keel resembles that of other vertebrates in many aspects. Oriented cell divisions coupled with oriented cell intercalations appear to be involved in the morphogenesis of the neural keel. Embryos mutant in the cyclops gene show deficiencies in the ventral neural tube. They lack the floor plate and the ventral parts of the diencephalon. Two recently cloned genes, axial and sonic hedgehog, have been implicated in the development of the ventral midline of the neural tube. Expression of axial and sonic hedgehog is impaired by the cyclops mutation in the midline of the neural plate. This, together with the effects of ectopic expression of the two cloned genes, suggests that axial, sonic hedgehog, and cyclops are part of the regulatory cascade leading to floor plate formation.

Animals↗
PubMed2005

Study on fish embryo responses to the treatment of cryoprotective chemicals using impedance spectroscopy.

Investigations using electrical impedance spectroscopy to measure the responses of fish embryos to the cryoprotective chemicals, methanol and dimethyl sulphoxide (DMSO), were carried out. Zebrafish (Danio rerio) embryos were used as a model to study the newly proposed technique. The normalised permittivity and conductivity changes of the embryos were measured continuously over a 20-min period in a customised embryo-holding chamber. The normalised permittivity and conductivity spectra were obtained during embryo exposure to different concentrations of methanol (1.0, 2.0 and 3.0 M) and DMSO (0.5, 1.0 and 2.0 M) solutions. The results showed significant permittivity and conductivity changes after embryo exposure to methanol and DMSO at the optimum embryo loading level (six embryos). Embryos in different concentrations of methanol and DMSO also resulted in quantitative responses shown in the normalised permittivity and conductivity spectra. The results demonstrated that fish embryo membrane permeability to cryoprotective chemicals could be monitored in real-time. The measurement of permittivity at a lower frequency range (10-10(3) Hz) and conductivity at a higher frequency range (10(4)-10(6) Hz) during fish embryo exposure to cryoprotective chemicals using impedance spectroscopy can be used as a new tool for the fast screening of most effective cryoprotective chemicals. The results from the present study also demonstrated the possibility of quantifying the level of cryoprotective chemicals penetrating the fish embryos.

Animals↗
PubMed2000

Genetic analysis of isometric growth control mechanisms in the zebrafish caudal Fin.

The body and fins of the zebrafish grow rapidly as juveniles and slower as they reach maturation. Throughout their lives, the fins grow isometrically with respect to the body. Growth of individual fin rays is achieved by the distal addition of bony segments. We have investigated the genetic control of mechanisms that initiate new segments or control size of newly initiated segments. We find that both segment initiation and segment length are regulated during fin growth in wild-type fish. We examined the growth properties of lof and sof fin length mutants for effects on the number and length of fin ray segments. Fins of lof mutants continue to grow rapidly even after wild-type fin growth slows, resulting in positive allometric growth and additional fin ray segments. We suggest that lof mutants bypass mechanisms that limit segment initiation. Isometric growth is retained in sof mutants, resulting in shorter fins one-half the length of wild-type fins. The primary defect in sof mutants is that fin ray segments are shorter than wild-type segments, although segment number is also diminished. Double mutants for sof;lof reveal that segment length and segment number are controlled in different pathways. Our findings suggest that the lof gene product regulates segment initiation and the sof gene product regulates segment length.

Aging↗
PubMed1999

Natural preference of zebrafish (Danio rerio) for a dark environment.

The zebrafish (Danio rerio) has been used as a model in neuroscience but knowledge about its behavior is limited. The aim of this study was to determine the preference of this fish species for a dark or light environment. Initially we used a place preference test and in a second experiment we applied an exit latency test. A two-chamber aquarium was used for the preference test. The aquarium consisted of a black chamber and a white chamber. In the first experiment the animal was placed in the aquarium and the time spent in the two compartments was recorded for 10 min. More time was spent in the black compartment (Wilcoxon matched-pairs signed-rank test, T = 7, N1 = N2 = 18, P = 0.0001). In the second experiment the animal was placed in the black or white compartment and the time it took to go from the initial compartment to the opposite one was recorded. The test lasted a maximum of 10 min. The results showed that the animal spent more time to go from the black to the white compartment (Mann-Whitney rank sum test, T = 48, N1 = 9, N2 = 8, P<0.0230). These data suggest that this fish species has a natural preference for a dark environment and this characteristic can be very useful for the development of new behavioral paradigms for fish.

Animals↗
PubMed2003

Dystrophin is required for the formation of stable muscle attachments in the zebrafish embryo.

A class of recessive lethal zebrafish mutations has been identified in which normal skeletal muscle differentiation is followed by a tissue-specific degeneration that is reminiscent of the human muscular dystrophies. Here, we show that one of these mutations, sapje, disrupts the zebrafish orthologue of the X-linked human Duchenne muscular dystrophy (DMD) gene. Mutations in this locus cause Duchenne or Becker muscular dystrophies in human patients and are thought to result in a dystrophic pathology through disconnecting the cytoskeleton from the extracellular matrix in skeletal muscle by reducing the level of dystrophin protein at the sarcolemma. This is thought to allow tearing of this membrane, which in turn leads to cell death. Surprisingly, we have found that the progressive muscle degeneration phenotype of sapje mutant zebrafish embryos is caused by the failure of embryonic muscle end attachments. Although a role for dystrophin in maintaining vertebrate myotendinous junctions (MTJs) has been postulated previously and MTJ structural abnormalities have been identified in the Dystrophin-deficient mdx mouse model, in vivo evidence of pathology based on muscle attachment failure has thus far been lacking. This zebrafish mutation may therefore provide a model for a novel pathological mechanism of Duchenne muscular dystrophy and other muscle diseases.

Amino Acid Sequence↗
PubMed2006

Myelin structure and composition in zebrafish.

To establish a standard for genotype/phenotype studies on the myelin of zebrafish (Danio rerio), an organism increasingly popular as a model system for vertebrates, we have initiated a detailed characterization of the structure and biochemical composition of its myelinated central and peripheral nervous system (CNS; PNS) tissues. Myelin periods, determined by X-ray diffraction from whole, unfixed optic and lateral line nerves, were approximately 153 and approximately 162 Angstrom, respectively. In contrast with the lability of PNS myelin in higher vertebrates, zebrafish lateral line nerve myelin exhibited structural stability when exposed to substantial changes in pH and ionic strength. Neither optic nor lateral line nerves showed swelling at the cytoplasmic apposition in CaCl(2)-containing Ringer's solution, in contrast with nerves from other teleost and elasmobranch fishes. Zebrafish optic nerve showed greater stability against changes in NaCl and CaCl(2) than lateral line nerve. The nerves from zebrafish having mutations in the gene for myelin basic protein (mbpAla2Thr and mbpAsp25Val) showed similar myelin periods as the wildtype (WT), but gave approximately 20% less compact myelin. Analysis of proteins by SDS-PAGE and Western blotting identified in both CNS and PNS of WT zebrafish two orthologues of myelin P0 glycoprotein that have been characterized extensively in trout--intermediate protein 1 (24 kDa) and intermediate protein 2 (28 kDa). Treatment with endoglycosidase-F demonstrated a carbohydrate moiety of approximately 7 kDa, which is nearly threefold larger than for higher vertebrates. Thin-layer chromatography for lipids revealed a similar composition as for other teleosts. Taken together, these data will serve as a baseline for detecting changes in the structure and/or amount of myelin resulting from mutations in myelin-related genes or from exogenous, potentially cytotoxic compounds that could affect myelin formation or stability.

Animals↗
PubMed2002

The zebrafish eye: developmental and genetic analysis.

In this review, we have attempted to cover all the major points of zebrafish eye development, and have found that, for the most part, it has much in common with other eyes, in both vertebrates and the fly. In addition to the confirmation and extension of earlier studies, however, the work on zebrafish has provided some new insights that should be assessed for their applicability to the development of other vertebrates. Among these are the modulated cellular proliferation in the optic vesicle, the complex spatiotemporal pattern of central retinal neurogenesis, the emergence of spatial order among the photoreceptors, the genetic controls of cell fates, and the genetic mechanisms underlying retinal stratification. Substantial though it is, this contribution will grow rapidly in the next few years as the advances of zebrafish genetics are accelerated by progress of genomics, especially the zebrafish genome project.

Animals↗
PubMed2003

The fates of zebrafish Hox gene duplicates.

In his 1970 book, Susumu Ohno stressed the importance of gene duplication in the evolution of the vertebrate genome and body plan. He elaborated the idea that duplication events provide novel genetic material on which evolution may act. Data are accumulating to show that extensive duplication events, perhaps incorporating the duplication of entire genomes, occurred in the lineage leading to teleost fishes. These duplications may have been pivotal in the explosive radiation of this highly successful vertebrate group. Thus, the teleosts provide us with an ideal opportunity to investigate the fates and functions of duplicated genes. A convenient system for these studies is the zebrafish, Danio rerio, which has become a popular genetic and embryological model.

Animals↗