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PubMed2005

Gene expression profiles of intact and regenerating zebrafish retina.

PURPOSE: Investigate the molecular determinants of retinal regeneration in adult vertebrates by analyzing the gene expression of control and post-lesion retina of adult zebrafish, a system that regenerates following injury. METHODS: Gene expression of zebrafish retina and brain were determined with DNA microarray, RT-PCR, and real-time quantitative PCR analyses. Damaged retinas and their corresponding controls were analyzed 2-5 days post-lesion (acute injury condition) or 14 d post-lesion (cell regeneration condition). RESULTS: Expected similarities and differences in the gene expression profile of zebrafish retina and brain were observed, confirming the applicability of the gene expression techniques. Mechanical lesion of retina triggered significant, time-dependent changes in retinal gene expression. The induced transcriptional changes were consistent with cellular phenomena known to occur, in a time-dependent manner, subsequent to retinal lesion, including cell cycle progression, axonal regeneration, and regenerative cytogenesis. CONCLUSIONS: The results indicate that retinal regeneration in adult zebrafish involves a complex set of induced, targeted changes in gene transcription, and suggest that these molecular changes underlie the ability of the adult vertebrate retina to regenerate.

Animals↗

PubMed2005

Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko.

PURPOSE: To determine the genomic organization of the zebrafish crx gene and to evaluate if mutations in crx are responsible for the retinal degeneration phenotype in the zebrafish (Danio rerio) mutants niezerka (nie(m743)) and mikre oko (mok(m632)). METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). Amplicons were sequenced and sequence data assembled into contigs. Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. Linkage analysis used DNA from mapping panels of single homozygous mutant animals with mixed genetic backgrounds. RESULTS: The analysis indicated that the zebrafish crx gene consisted of three exons and 2 introns, and spans 3.8 kb of genomic DNA. The splice junctions were all located within the coding region. Highly repetitive sequences present in non-coding regions of crx and extended tetra-nucleotide repeats in intronic regions were associated with sequence variation between different strains. Homozygous mok(m632) or nie(m743) mutants and their respective wild-type sibs, showed identical patterns of heterozygosity and sequence variations within each line. No mutation in crx were identified in homozygous mok(m632) or nie(m743). Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. CONCLUSIONS: Despite the presence of sequence variations in their respective genetic backgrounds, within each line the sequence of crx was identical. Consistent with the absence of mutations, further analysis excluded linkage of the mutant phenotypes to crx. Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines.

Animals↗

PubMed2006

[Research progress on cell apoptosis during embryonic development of the zebrafish (Danio rerio)].

Cells have a built-in death program through the regulation of genes. Apoptosis (programmed cell death) plays a very important role in the development of the vertebrate embryo. The zebrafish (Danio rerio) has become a useful and ideal model in molecular developmental biology for in vivo study on the function of apoptosis in morphogenesis, sex differentiation and so on, and has already been garnering more and more attention. At present, much progress has been made regarding apoptotic pathways in zebrafish development. Caspases and other regulatory apoptotic genes have been cloned successfully. Moreover, transgenic zebrafish embryos have been induced to undergo apoptosis in vivo to study apoptotic signaling pathways and the abnormal morphological changes during embryogenesis. Transgenic zebrafish has provided a powerful tool for illuminating the interaction between regulatory apoptotic genes and vertebrate development.

Animals↗

PubMed2006

Assessment of xenoestrogens using three distinct estrogen receptors and the zebrafish brain aromatase gene in a highly responsive glial cell system.

The brain cytochrome P450 aromatase (Aro-B) in zebrafish is expressed in radial glial cells and is strongly stimulated by estrogens (E2); thus, it can be used in vivo as a biomarker of xenoestrogen effects on the central nervous system. By quantitative real-time polymerase chain reaction, we first confirmed that the expression of Aro-B gene is robustly stimulated in juvenile zebrafish exposed to several xenoestrogens. To investigate the impact of environmental estrogenic chemicals on distinct estrogen receptor (ER) activity, we developed a glial cell-based assay using Aro-B as the target gene. To this end, the ER-negative glial cell line U251-MG was transfected with the three zebrafish ER subtypes and the Aro-B promoter linked to a luciferase reporter gene. E2 treatment of U251-MG glial cells cotransfected with zebrafish ER-alpha and the Aro-B promoter-luciferase reporter resulted in a 60- to 80-fold stimulation of luciferase activity. The detection limit was <0.05 nM, and the EC50 (median effective concentration) was 1.4 nM. Interestingly, in this glial cell context, maximal induction achieved with the Aro-B reporter was three times greater than that observed with a classical estrogen-response-element reporter gene (ERE-tk-Luc). Dose-response analyses with ethynylestradiol (EE2), estrone (E1), alpha-zeralenol, and genistein showed that estrogenic potency of these agents markedly differed depending on the ER subtype in the assay. Moreover, the combination of these agents showed an additive effect according to the concept of concentration addition. This confirmed that the combined additive effect of the xenoestrogens leads to an enhancement of the estrogenic potency, even when each single agent might be present at low effect concentrations. In conclusion, we demonstrate that our bioassay provides a fast, reliable, sensitive, and efficient test for evaluating estrogenic potency of endocrine disruptors on ER subtypes in a glial context.

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PubMed2005

Transcriptome analysis of zebrafish embryogenesis using microarrays.

Zebrafish (Danio rerio) is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula) revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html).

Journal Article↗

PubMedDate not supplied

Chilling sensitivity in zebrafish (Brachydanio rerio) oocytes is related to lipid phase transition.

Oocytes of zebrafish were used to study chilling sensitivity and membrane lipid phase transitions in tropical fish. The oocytes were divided into two groups: small (without yolk, <0.1mm) and large (with yolk, >0.1mm). After exposure of the oocytes to different temperatures (25, 22, 19, 16, 12, 8, 0, -8+0.5 degree C) for 15 minutes, the integrity of their membranes was determined by carboxyfluorescein diacetate (CFDA) staining. At 16 and 12 degree C, damage was maximum (membrane integrity decreased by 50%) for small and large sizes, respectively. Lipid phase transition (LPT), which was evaluated using Fourier transform infrared (FTIR) microscopy, indicated phase transitions at the same temperatures at which damage was maximal (between 22 and 12 degree C).In another series of experiments, the chilling sensitivity of oocytes taken from zebrafish which had been held at 16 degree C for different periods of time (0, 15, 30, 60 minutes) was determined as described above. In small oocytes membrane integrity decreased after 15 minutes, and in large oocytes integrity decreased after 30 minutes. Chilling sensitivity was also measured in oocytes from zebrafish that had been held at 16 degree C for 30 minutes and then rewarmed to 28 degree C for 2 hours. Despite this recovery period, the integrity of the oocytes remained low. We suggest that chilling sensitivity in zebrafish oocytes is related to lipid phase transition of their membranes and starts at 10 degree C below the physiological temperature

Journal Article↗

PubMed1998

Restricted expression of the neuronal intermediate filament protein plasticin during zebrafish development.

In the adult goldfish visual pathway, expression of the neuronal intermediate filament (nIF) protein plasticin is restricted to differentiating retinal ganglion cells (RGCs) at the margin of the retina. Following optic nerve injury, plasticin expression is elevated transiently in all RGCs coincident with the early stages of axon regeneration. These results suggest that plasticin may be expressed throughout the nervous system during the early stages of axonogenesis. To test this hypothesis, we analyzed plasticin expression during zebrafish (Danio rerio) neuronal development. By using immunocytochemistry and in situ hybridization, we found that plasticin is expressed in restricted subsets of early zebrafish neurons. Expression coincides with axon outgrowth in projection neurons that pioneer distinct axon tracts in the embryo. Plasticin is expressed first in trigeminal, Rohon-Beard, and posterior lateral line ganglia neurons, which are among the earliest neurons to initiate axonogenesis in zebrafish. Plasticin is expressed also in reticulospinal neurons and in caudal primary motoneurons. Together, these neurons establish the first behavioral responses in the embryo. Plasticin expression also coincides with initial RGC axonogenesis and progressively decreases after RGC axons reach the tectum. At later developmental stages, plasticin is expressed in a subset of the cranial nerves. The majority of plasticin-positive neurons are within or project axons to the peripheral nervous system. Our results suggest that plasticin subserves the changing requirements for plasticity and stability during axonal outgrowth in neurons that project long axons.

Animals↗

PubMed1999

Analysis of a Zebrafish semaphorin reveals potential functions in vivo.

The semaphorin/collapsin gene family is a large and diverse family encoding both secreted and transmembrane proteins, some of which are thought to act as repulsive axon guidance molecules. However, the function of most semaphorins is still unknown. We have cloned and characterized several semaphorins in the zebrafish in order to assess their in vivo function. Zebrafish semaZ2 is expressed in a dynamic and restricted pattern during the period of axon outgrowth that indicates potential roles in the guidance of several axon pathways. Analysis of mutant zebrafish with reduced semaZ2 expression reveals axon pathfinding errors that implicate SemaZ2 in normal guidance.

Amino Acid Sequence↗

PubMed1999

Characterization of zebrafish primordial germ cells: morphology and early distribution of vasa RNA.

Research into germ line development is of conceptual and biotechnologic importance. In this study, we used morphology at the level of light and electron microscope to characterize the primordial germ cells (PGCs) of the zebrafish throughout embryonic and larval development. The study was complemented by the detailed analysis of mRNA expression of a putative germ line marker vasa. By morphology alone PGCs were identified at the earliest at the 5-somite stage in the peripheral endoderm in contact with the yolk syncytial layer. Subsequently, they move from lateral to medial positions into the median mesoderm and from there by means of the dorsal mesentery into the gonadal anlage at day 5 postfertilization (pf), to establish gonads with mesenchymal cells by day 9 pf. Ultrastructural analysis of the 4-day-old zebrafish larvae demonstrates the presence of the germ line-specific structures, nuage, and annulate lamellae. vasa RNA-positive cells can be followed during zebrafish embryogenesis from the 32-cell stage onward (Yoon et al., 1997). Upon completion of gastrulation, the RNA is exclusively present in the cells of the hypoblast, which as a consequence of convergence and extension movements first arrange themselves in a V-shaped string-like conformation to end up, by late somitogenesis, as a string of cells on each side of the midline. We show that the localization of maternal vasa RNA in the ovary changes from cytoplasmic, in the previtellogenic oocytes, to cortical in the vitellogenic oocytes, to concentrate at the boundary of the yolk and cytoplasm in the one cell stage zygote. These results demonstrate that the cortical vasa RNA localization precedes its cleavage furrow-associated localization in the embryos and is presumably cytoskeleton dependent. vasa RNA localization changes from asymmetric subcellular at the sphere stage, to become entirely cytoplasmic at the dome stage. These data suggest a close resemblance in modes of segregation of the germ plasma in the frog and vasa mRNA in the fish during cleavage stages. Based on the significantly larger size and the stereotype and similar position of morphologically distinct cells, presumed to be PGCs, and their vasa RNA-positive counterparts, we conclude that vasa RNA-positive cells are the PGCs and vasa RNA represents a definitive germ line marker in the fish. Dev Dyn 1999;216:153-167.

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PubMed2000

Vertebrate model systems in the study of early heart development: Xenopus and zebrafish.

Xenopus and zebrafish serve as outstanding models in which to study vertebrate heart development. The embryos are transparent, allowing observation during organogenesis; they can be obtained in large numbers; and they are readily accessible to embryologic manipulation and microinjection of RNA, DNA, or protein. These embryos can live by diffusion for several days, allowing analysis of mutants or experimental treatments that perturb normal heart development. Xenopus embryos have been used to understand the induction of the cardiac field, the role of Nkx genes in cardiac development, and the role transforming growth factor beta molecules in the establishment and signaling of left-right axis information. Large-scale mutant screens in zebrafish and the development of transgenics in both Xenopus and zebrafish have accelerated the molecular identification of genes that regulate conserved steps in cardiovascular development.

Animals↗

PubMed2001

Specific pan-neural crest expression of zebrafish Crestin throughout embryonic development.

Zebrafish crestin was identified in a screen for genes dependent on cyclops function and is a member of a family of retroelements (Rubinstein et al. [2000] Genesis 26:86-97). We report here a detailed description of crestin mRNA expression during zebrafish embryogenesis. Crestin expression was first observed during the onset of somitogenesis in cells of the neural crest domain of the ectoderm. Crestin expression was subsequently observed in premigratory cranial and trunk neural crest cells and then in actively migrating crest cells. Cell counts of crestin-expressing premigratory trunk neural crest cells strongly suggest that crestin is expressed by all neural crest cells at this stage. Crestin expression co-localized with a battery of markers for premigratory neural crest cells, developmentally distinct neural crest-derived precursor sublineages, and overtly differentiated neural crest-derived cell types. Expression of crestin is gradually downregulated in overtly differentiated cells. Our results indicate that crestin is a specific pan-neural crest marker throughout zebrafish embryogenesis.

Animals↗

PubMed2000

Zebrafish nma is involved in TGFbeta family signaling.

Bone morphogenetic proteins (BMP) are members of the TGFbeta superfamily of secreted factors with important regulatory functions during embryogenesis. We have isolated the zebrafish gene, nma, that encodes a protein with high sequence similarity to human NMA and Xenopus Bambi. It is also similar to TGFbeta type I serine/theronine kinase receptors in the extracellular ligand-binding domain but lacks a cytoplasmic kinase domain. During development, nma expression is similar to that of bmp2b and bmp4, and analysis in the dorsalized and ventralized zebrafish mutants swirl and chordino indicates that nma is regulated by BMP signaling. Overexpression of nma during zebrafish and Xenopus development resulted in phenotypes that appear to be based on inhibition of BMP signaling. Biochemically, NMA can associate with TGFbeta type II receptors and bind to TGFbeta ligand. We propose that nma is a BMP-regulated gene whose function is to attenuate BMP signaling during development through interactions with type II receptors and ligands.

Activin Receptors, Type I↗

PubMed2004

Identification and morphogenesis of the eminentia thalami in the zebrafish.

This study documents early zebrafish brain expression patterns (2-5 days postfertilization) of proliferating neural (PCNA) as well as early-determined (Pax6, Zash-1a, Zash-1b, neurogenin1, neuroD) and differentiating (Hu-proteins) neuronal cells. These patterns are used to outline the spatiotemporal local dynamics of secondary neurogenesis as well as neuronal migration and differentiation in the region of the eminentia thalami. The analysis presented not only allows identification for the first time of the eminentia thalami in the zebrafish model system (because it forms a neurogenin1/neuroD-guided locus of neurogenesis in contrast to adjacent preoptic region and ventral thalamus) but furthermore shows that the entopeduncular complex is a derivative of the embryonic zebrafish eminentia thalami, which has never been reported for a teleost before. An analysis of the relevant literature shows that the mammalian entopeduncular nucleus/avian paleostriatum primitivum/reptilian globus pallidus clearly are part of the basal ganglia (i.e., the pallidum). In amniote embryos, an anterior entopeduncular area is recognized at the base of the medial ganglionic eminence (i.e., the future pallidum; part of alar plate of prosomere 5), separate from the more posterior eminentia thalami (alar prosomere 4). There is a comparable periventricular eminentia thalami in (young and adult) amphibians and teleosts. However, the migrated anterior entopeduncular nucleus of anuran amphibians likely is homologous to part of the pallidum of other vertebrates and has no developmental relationship to the eminentia thalami. In contrast, the migrated teleostean entopeduncular complex does not correspond to a pallidal division but is indeed the adult derivative of the early-recognized eminentia thalami as shown in this study.

Animals↗

PubMed2006

Calretinin immunoreactivity in the brain of the zebrafish, Danio rerio: distribution and comparison with some neuropeptides and neurotransmitter-synthesizing enzymes. II. Midbrain, hindbrain, and rostral spinal cord.

The distribution of calretinin (CR) in the brainstem and rostral spinal cord of the adult zebrafish was studied by using immunocytochemical techniques. For analysis of some brainstem nuclei and regions, CR distribution was compared with that of complementary markers (choline acetyltransferase, glutamic acid decarboxylase, tyrosine hydroxylase, neuropeptide Y). The results reveal that CR is a marker of various neuronal populations distributed throughout the brainstem, including numerous cells in the optic tectum, torus semicircularis, secondary gustatory nucleus, reticular formation, somatomotor column, gustatory lobes, octavolateral area, and inferior olive, as well as of characteristic tracts of fibers and neuropil. These results indicate that CR may prove useful for characterizing a number of neuronal subpopulations in zebrafish. Comparison of the distribution of CR observed in the brainstem of zebrafish with that reported in an advanced teleost (the gray mullet) revealed a number of similarities, and also some interesting differences. Our results indicate that many brainstem neuronal populations have maintained the CR phenotype in widely divergent teleost lines, so CR studies may prove very useful for comparative analysis.

Animals↗

PubMed2002

Green fluorescent protein expression in germ-line transmitted transgenic zebrafish under a stratified epithelial promoter from keratin8.

A zebrafish cDNA encoding a novel keratin protein was characterized and named keratin8, or krt8. krt8 expression was initiated at 4.5 hr postfertilization, immediately after the time of zygotic genome activation. The expression is limited to a single layer of envelope cells on the surface of embryos and, in later stages, it also appears in the innermost epithelial layer of the anterior- and posteriormost portions of the digestive tract. In adult, its expression was limited to the surface layer of stratified epithelial tissues, including skin epidermis and epithelia of mouth, pharynx, esophagus, and rectum but not in the gastral and intestinal epithelia. By using a 2.2-kb promoter from krt8, several stable green fluorescent protein (gfp) transgenic zebrafish lines were established. All of these transgenic lines displayed GFP expression in tissues mentioned above except for the rectum; therefore, the pattern of transgenic GFP expression is essentially identical to that of the endogenous krt8 mRNAs. krt8-GFP fusion protein was also expressed in zebrafish embryos under a ubiquitous promoter, and the fusion protein was capable of assembling into intermediate filaments only in the epithelia that normally expressed krt8 mRNAs, indicating the specificity of keratin assembly in vivo.

Amino Acid Sequence↗

PubMed2002

Molecular characterization of Calymmin, a novel notochord sheath-associated extracellular matrix protein in the zebrafish embryo.

During the screening of a zebrafish postsomitogenesis embryo cDNA library, we have identified a cDNA corresponding to a novel type of protein localized to the notochordal sheath-associated extracellular matrix (ECM) of the embryo. The 4.049-kb mRNA encodes a predicted polypeptide of 1,207 amino acids (122 kDa, pI 10.50) with a potential signal peptide of 20 amino acids. After the signal peptide, the mature protein consists of 1,187 amino acids (119 kDa, pI 10.46), for which the name "Calymmin" (from Greek chialphalambdanumumualpha, to envelop, to cover) is proposed. The Calymmin mRNA is highly and transiently expressed by the notochord cells of the embryo from the 10- to 12-somite stage to the pharyngula period (13 and 24 hours postfertilization, respectively), and light and electron microscopical immunolocalization analysis revealed that the protein was specifically localized within a granular and filamentous layer of the ECM compartment surrounding the notochord. In zebrafish no tail mutants (ntl(tc41)), in which the notochord precursor cells are present but fail to differentiate, the Calymmin protein was not detected, confirming the notochord origin of Calymmin. These results indicate that Calymmin is a novel constitutive protein of the ECM compartment associated to the perinotochordal sheath in the zebrafish embryo, which is specifically expressed by the differentiating notochord cells.

Amino Acid Sequence↗

PubMed2002

A zebrafish unc-45-related gene expressed during muscle development.

We report the isolation and expression pattern of zebrafish unc45r, a gene related to Caenorhabditis elegans unc-45. UNC-45 is a muscle-specific protein thought to interact with myosin and promote the assembly of muscle thick filaments during C. elegans development. Zebrafish Unc45r shares sequence features with C. elegans UNC-45, including three tetratricopeptide repeats and a CRO1/She4p homology domain. unc45r is expressed in mesoderm adjacent to the dorsal midline during late gastrula stages and is coexpressed with muscle specific genes in somitic mesoderm during development of trunk skeletal muscle. unc45r is also expressed in cranial skeletal muscle as well as in cardiac and smooth muscle. The isolation of a muscle-specific unc-45 related gene from zebrafish suggests a common mechanism for muscle filament assembly between vertebrates and invertebrates.

Amino Acid Sequence↗

PubMed2003

Differential expression of Na,K-ATPase alpha and beta subunit genes in the developing zebrafish inner ear.

We have used whole-mount in situ hybridization to analyze Na,K-ATPase alpha and beta subunit gene expression in the developing zebrafish ear. Four alpha1-like (alpha1a.1, alpha1a.2, alpha1a.4, and alpha1a.5) and two beta (beta1a and beta2b) subunit genes are expressed in ear beginning at mid-somitogenesis. Each gene exhibits a distinct spatial and temporal expression pattern. The alpha1a.1 gene was ubiquitously expressed in the otic epithelium from mid-somitogenesis to 24 hr postfertilization (hpf). Expression of this gene was gradually reduced and by 48 hpf, alpha1a.1 transcripts were no longer detectable in the ear. The alpha1a.2 and alpha1a.5 genes were expressed in regions that correspond to the anterior macula, lateral crista, and semicircular canal projections up to 48 hpf. At later stages, expression of these genes was limited to cells in the dorsolateral septum and semicircular canal projections. alpha1a.4 and beta1a transcripts were ubiquitously expressed during ear development and were present in most otic tissues at 5 days postfertilization (dpf). Expression of the beta2b gene, on the other hand, was restricted to subsets of cells that form sensory epithelia. These results strongly suggest different functional roles for individual Na,K-ATPase genes in zebrafish ear development. Na,K-ATPase genes are likely to represent useful markers for the analysis of zebrafish otogenesis.

Animals↗