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PubMed2002

Patterning the zebrafish central nervous system.

We have described the formation of the zebrafish central nervous system. The spinal cord has the simplest organization and was considered first, followed by the forebrain, midbrain and hindbrain. We have discussed many studies that have revealed the molecular mechanisms, including extrinsic signals and intrinsic responses to them, underlying the establishment of nervous system regions and the wide diversity of neuronal cell types of which they are comprised. Wherever possible, we have tried to compare what has been learned from zebrafish with what is known in other vertebrate species. The simplicity of the developing nervous system makes zebrafish embryos particularly amenable to studies of nervous system development. Thus, many aspects of nervous system patterning that were unknown from other vertebrates have been revealed by studies in zebrafish. However, the relationship between embryonic and adult nervous system morphology is still not entirely clear and remains an important avenue for further studies.

Animals↗
PubMed2006

Cranial neural crest and development of the head skeleton.

The skeletal derivatives of the cranial neural crest (CNC) are patterned through a combination of intrinsic differences between crest cells and extrinsic signals from adjacent tissues, including endoderm and ectoderm. In this chapter, we focus on how CNC cells positionally interpret these cues to generate such highly specialized structures as the jaw and ear ossicles. We highlight recent genetic studies of craniofacial development in zebrafish that have revealed new tissue interactions and show that the process of CNC development is highly conserved across the vertebrates.

Animals↗
PubMed2004

When sugars guide axons: insights from heparan sulphate proteoglycan mutants.

Although there have previously been hints that heparan sulphate proteoglycans (HSPGs) are important for axon guidance, as they are for many other biological processes, there has been little in vivo evidence for interaction with known axon-guidance pathways. Genetic analyses of fly, mouse, nematode and zebrafish mutants now confirm the role of HSPGs in axon guidance and are beginning to show that they might have a key role in modulating the action of axon-guidance ligands and receptors.

Animals↗
PubMed2006

Conserved and acquired features of adult neurogenesis in the zebrafish telencephalon.

Our understanding of the cellular and molecular mechanisms underlying the adult neural stem cell state remains fragmentary. To provide new models on this issue, we searched for stem cells in the adult brain of the zebrafish. Using BrdU tracing and immunodetection of cell-type-specific markers, we demonstrate that the adult zebrafish telencephalon contains self-renewing progenitors, which show features of adult mammalian neural stem cells but distribute along the entire dorso-ventral extent of the telencephalic ventricular zone. These progenitors give rise to newborn neurons settling close to the ventricular zone within the telencephalon proper. They have no equivalent in mammals and therefore constitute a new model of adult telencephalic neural stem cells. In addition, progenitors from the ventral subpallium generate rapidly dividing progenitors and neuroblasts that reach the olfactory bulb (OB) via a rostral migratory stream and differentiate into GABAergic and TH-positive neurons. These ventral progenitors are comparable to the mammalian neural stem cells of the subependymal zone. Interestingly, dorsal and ventral progenitors in the adult telencephalon express a different combination of transcription factors than their embryonic counterparts. In the case of neurogenin1, this is due to the usage of different enhancer elements. Together, our results highlight the conserved and unique phylogenic and ontogenic features of adult neurogenesis in the zebrafish telencephalon and open the way to the identification of adult neural stem cell characters in cross-species comparative studies.

Age Factors↗
PubMed2002

Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis.

Warm-blooded vertebrates show large-scale variation in G + C content along their chromosomes, a pattern which appears to be largely absent from cold-blooded vertebrates. However, compositional variation in poikilotherms has generally been studied by ultracentrifugation rather than sequence analysis. In this paper, we investigate the compositional properties of coding sequences from a broad range of vertebrate poikilotherms using DNA sequence analysis. We find that on average poikilotherms have lower third-codon position GC contents (GC3) than homeotherms but that some poikilotherms have higher mean GC3 values. We find that most poikilotherms have lower variation in GC3 than homeotherms but that there is a correlation between GC12 and GC3 for some species, indicating that there is systematic variation in base composition across their genomes. We also demonstrate that the GC3 of genes in the zebrafish, Danio rerio, is correlated with that in humans, suggesting that vertebrates share a basic isochore structure. However, we find no correlation between either the mean GC3 or the standard deviation in GC3 and body temperature.

Animals↗
PubMed1999

Dissecting hematopoiesis and disease using the zebrafish.

The study of blood has often defined paradigms that are relevant to the biology of other vertebrate organ systems. As examples, stem cell physiology and the structure of the membrane cytoskeleton were first described in hematopoietic cells. Much of the reason for these successes resides in the ease with which blood cells can be isolated and manipulated in vitro. The cell biology of hematopoiesis can also be illuminated by the study of human disease states such as anemia, immunodeficiency, and leukemia. The sequential development of the blood system in vertebrates is characterized by ventral mesoderm induction, hematopoietic stem cell specification, and subsequent cell lineage differentiation. Some of the key regulatory steps in this process have been uncovered by studies in mouse, chicken, and Xenopus. More recently, the genetics of the zebrafish (Danio rerio) have been employed to define novel points of regulation of the hematopoietic program. In this review, we describe the advantages of the zebrafish system for the study of blood cell development and the initial success of the system in this pursuit. The striking similarity of zebrafish mutant phenotypes and human diseases emphasizes the utility of this model system for elucidating pathophysiologic mechanisms. New screens for lineage-specific mutations are beginning, and the availability of transgenics promises a better understanding of lineage-specific gene expression. The infrastructure of the zebrafish system is growing with an NIH-directed genome initiative, providing a detailed map of the zebrafish genome and an increasing number of candidate genes for the mutations. The zebrafish is poised to contribute greatly to our understanding of normal and disease-related hematopoiesis.

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↗
PubMed2004

Amino acids runs and genomic compositional biases in vertebrates.

A compositional analysis of a sample of 50 zebrafish proteins containing at least one alanine run and of their open reading frames (ORFs) has been performed. The sample of poly(Ala) proteins showed a tendency to have runs of other amino acids (His/H, Gln/Q, Ser/S, Pro/P). Their ORFs and the first and second codon positions had higher GC contents than a reference gene set. The "universal" correlation between the GC content of the first+second and third codon positions (GC1+2 vs GC3) does not hold, but I provide an explanation in terms of genomic heterogeneity. Significant correlation between AHQS content and GC3 was obtained, reflecting codon bias favoring G/C at the third codon position of these amino acids. A correspondence analysis (COA) of relative synonymous codon usage showed that the poly(Ala) proteins have a biased distribution according to the second axis of the COA, which correlates with gene expression in zebrafish. A comparison with human is undertaken.

Amino Acids↗
PubMed2004

accordion, a zebrafish behavioral mutant, has a muscle relaxation defect due to a mutation in the ATPase Ca2+ pump SERCA1.

When wild-type zebrafish embryos are touched at 24 hours post-fertilization (hpf), they typically perform two rapid alternating coils of the tail. By contrast, accordion (acc) mutants fail to coil their tails normally but contract the bilateral trunk muscles simultaneously to shorten the trunk, resulting in a pronounced dorsal bend. Electrophysiological recordings from muscles showed that the output from the central nervous system is normal in mutants, suggesting a defect in muscles is responsible. In fact, relaxation in acc muscle is significantly slower than normal. In vivo imaging of muscle Ca2+ transients revealed that cytosolic Ca2+ decay was significantly slower in acc muscle. Thus, it appears that the mutant behavior is caused by a muscle relaxation defect due to the impairment of Ca2+ re-uptake. Indeed, acc mutants carry a mutation in atp2a1 gene that encodes the sarco(endo)plasmic reticulum Ca2+-ATPase 1 (SERCA1), a Ca2+ pump found in the muscle sarcoplasmic reticulum (SR) that is responsible for pumping Ca2+ from the cytosol back to the SR. As SERCA1 mutations in humans lead to Brody disease, an exercise-induced muscle relaxation disorder, zebrafish accordion mutants could be a useful animal model for this condition.

Amino Acid Sequence↗
PubMed1999

Germ line development in fishes.

Classical work on germ cells in fishes has dealt with three main issues; their embryonic origin, the proliferation, and migration pathway during embryonic and larval development. Until recently, primordial germ cells (PGCs) have been studied in a number of fishes using morphological criteria only. The identification of the Drosophila vasa homolog gene of zebrafish now allows comparison of these morphological data with vasa RNA expression patterns in zebrafish. Teleost PGCs can be distinguished from somatic cells by their distinct morphology, at the earliest during gastrulation, and in most fishes their number varies between 10 and 30 during pregonial development. Mitosis is generally not observed in PGCs at extragonadal locations, whereas they are mitotically active once at the gonadal ridges. During gastrulation, PGCs appear to translocate from the epiblast to the hypoblast and during somitogenesis they are found associated with the most peripheral yolk syncitial layer (YSL). From the peripheral YSL they migrate through the median mesoderm into the dorsal mesoderm and then to the dorsal mesentery, where they establish the gonad primordia with mesenchymal cells. Vasa RNA positive cells, the PGCs of the zebrafish conform to these general observations. Interestingly, classical descriptive and experimental data can now be reevaluated using vasa as a molecular marker of the fish germ line. The power of zebrafish genetics together with possibilities of experimental embryology should accelerate research on aspects of vertebrate germ line development such as PGC migration, division and apoptosis, as well as (in) fertility. The present review summarizes some of the classical data on germ line development in fishes in relation to recent data on vasa expression in zebrafish and compares these findings, where appropriate, with those in other model organisms. Special emphasis is placed on vasa gene expression as a potential universal germ line marker and suggestions are made for novel, zebrafish specific approaches to investigate the vertebrate germ line.

Animals↗
PubMed1998

Use of the zebrafish (Danio rerio) to define hematopoiesis.

Hematopoiesis in the vertebrate is characterized by the induction of ventral mesoderm to form hematopoietic stem cells and the eventual differentiation of these progenitors to form the peripheral blood lineages. Several genes have been implicated in the differentiation and development of hematopoietic and vascular progenitor cells, yet our understanding of the discrete steps involved in the induction of these cells from the ventral mesoderm is still incomplete. One method of delineating these processes is based on the use of lower vertebrates. The zebrafish (Danio rerio) is an especially robust vertebrate system for both isolating and characterizing genes involved in these processes. Hematopoietic mutants have been generated with defects in many of the steps of both the primitive and definitive hematopoietic programs. Cloning of the genes that underlie these mutations should yield valuable details of hematopoiesis and may have therapeutic implications for bone marrow transplantation and stem cell gene therapy.

Animals↗
PubMed2006

Blocking expression of AHR2 and ARNT1 in zebrafish larvae protects against cardiac toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin.

The zebrafish (Danio rerio) has become an attractive vertebrate model for studying developmental processes, and is emerging as a model system for studying the mechanisms by which xenobiotic compounds perturb normal development. Embryos treated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) shortly after fertilization exhibit a range of adverse effects on the heart: an early reduction in cardiac myocyte number, followed by a change in heart looping and morphology, with an apparent compaction of the ventricle and overall decrease in heart size. These changes are accompanied by impaired cardiac function including a decrease in cardiac output and eventually irreversible ventricular standstill. The mechanisms involved in mediating effects of TCDD on the heart remain unknown. However, it is widely accepted that aryl hydrocarbon receptor (AHR) activation mediates endpoints of TCDD toxicity in vertebrates. In zebrafish, there are multiple forms of AHR and AHR nuclear translocator protein (ARNT) raising the question about whether different endpoints of TCDD toxicity are mediated by different components of the AHR/ARNT pathway. To address this question we used morpholino oligonucleotide technology to specifically block the expression of zfAHR2, zfARNT1, zfARNT2, and zfCYP1A, and assessed the previously described effects of TCDD on heart morphology, size, and function in the developing morphants. We report that blocking zfAHR2 and zfARNT1 expression provided protection against the TCDD-mediated alteration in heart morphology, reduced cardiac myocyte number, decreased cardiac output and ventricular standstill in zebrafish larvae, while the zfarnt2 and zfcyp1a morpholinos did not block the TCDD-induced cardiac toxicity.

Animals↗
PubMed2026

Evolutionary Reorganization of Transcriptomic Architecture Across a UVB Tolerance Gradient in Fish.

Environmental stressors such as ultraviolet radiation impose strong selective pressures on organisms, yet how adaptation to such stressors shapes transcriptomic responses at the network level remains poorly understood. Although stratospheric ozone is recovering globally, substantial regional variation in UV exposure persists, particularly in high-altitude environments where extreme UV levels can occur. Here, we compared three fish models representing distinct biological responses to UVB exposure: wild-type zebrafish (Danio rerio), a melanin-deficient zebrafish mutant (nacre) lacking a major protective mechanism against UVB damage, and the high-altitude Andean killifish Orestias ascotanensis, a species naturally exposed to extreme UVB radiation. Together, these models define a gradient spanning physiological protection, impaired protection, and evolutionary adaptation to UVB stress. Using RNA-seq and protein-protein interaction networks, we show that transcriptomic responses differ markedly across this gradient. Wild-type and nacre zebrafish exhibited relatively limited transcriptomic changes (∼2%-2.4% of genes changing), whereas O. ascotanensis displayed a large-scale and highly coordinated response (∼21.6% of genes changing) characterized by functionally specialized networks enriched in DNA repair pathways. These differences involved not only transcriptomic magnitude but also marked reorganization of transcriptomic architecture. Integration with positive selection analyses revealed that positively selected genes were concentrated within highly interconnected regions of transcriptomic networks, consistent with adaptation involving network reorganization. Furthermore, ortholog-based analyses suggest that adaptive responses involve differential reorganization of a conserved functional background. Together, our results support a model in which adaptation to environmental stress is associated with the reorganization of conserved transcriptomic networks across physiological and evolutionary contexts, providing a systems-level perspective on the molecular basis of adaptation.

UVB radiation↗
PubMed2005

Analysis of cell movements in zebrafish embryos: morphometrics and measuring movement of labeled cell populations in vivo.

Cell movements occur in all phases of animal life from embryogenesis, to maintaining adult organs, to comprising a critical component of pathology. During gastrulation, cells demonstrate a repertoire of morphogenetic movements coordinated with fate inductions to sculpt the embryonic body. The morphogenetic behaviors, underlying mechanisms, and their control, are the subject of much current study. External development of the transparent zebrafish embryo, the abundance of mutations influencing cell movements, as well as a range of observation and manipulation methods, make the zebrafish valuable for cell movement studies. This chapter offers a conceptual background for analysis of gastrulation cell movements by reviewing how region specific cell movements shape the wild-type zebrafish embryo, and how defective morphogenetic movements alone or in combination with altered cell fate specification distort the body plans of known zebrafish mutants. We furnish methods for the morphometric analysis of embryonic shape and organ rudiments in live and fixed embryos, and present data collected from live wild-type, dorsoventral patterning (somitabun and chordino) and convergence and extension (knypek and trilobite) classes of mutants. We provide a method for quantitative assessment of the movements of cell populations in vivo, and a method for determining whether cell fate and/or movement are disturbed.

Animals↗
PubMed1998

Preparation and imaging of nuclear spreads from cells of the zebrafish embryo. Evidence for large degradation intermediates in apoptosis.

We describe a method for preparing nuclear spreads from cells of live, unfixed zebrafish embryos at the late-gastrula (approximately 8000 cell) stage of development. The method consists of a sequence of four steps: (1) a slow, gentle lysis, in low to moderate salt concentration, of cells and then nuclei, to release DNA-containing fibres; (2) spreading of the released fibres by a transverse fluid flow; (3) electrostatic, and possibly also covalent, attachment of the spread fibers to poly(L-lysine)-coated glass microscope slides; and (4) continued incubation to produce periodic cleavage of the DNA within the fibres, apparently through activation of endogenous nucleases. The nuclear spreads are imaged with epifluorescence, at a spatial resolution approaching the Rayleigh limit (approximately 230 nm for blue light). The epifluorescent signal is provided from Hoechst 33,258 bound specifically to the DNA, from a dye-coupled antibody conjugate bound specifically to histone H1 in the fibres, or from a DNA nick end-labelling assay. The spontaneous cleavage of DNA-containing fibres in step (4) of the above procedure can be blocked by the chelating agents EGTA and EDTA, by the caspase-2,3,7 inhibitor N-acetyl-Asp-Glu-Val-Asp-aldehyde, and by the caspase-1,4,5 inhibitors N-acetyl-Tyr-Val-Ala-Asp-aldehyde and N-acetyl-Tyr-Val-Ala-Asp-chloromethyl ketone. These data suggest that the spontaneous cleavage of fibres is catalysed by nucleases that become activated through a caspase-mediated mechanism. The involvement of caspase-dependent nucleases would suggest that an apoptosis pathway is activated in the spreads during their prolonged incubation. If bona fide apoptosis is induced in living zebrafish embryos by treatment with camptothecin (a topoisomerase I poison), and then nuclear spreads are prepared, we observe a similar fragmentation of the spread fibres. However, in this case the fragmentation is more rapid and complete. We hypothesize that, during the early phase of apoptosis, one or more endogenous nucleases are activated by a caspase-mediated mechanism. The nuclease(s) then specifically recognize and cleave a susceptible, periodically repeating feature of interphase chromatin.

Animals↗