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At least 1,099 records · Page 61Linked to original sources
PubMed2000

Drinks like a fish: zebra fish (Danio rerio) as a behavior genetic model to study alcohol effects.

Zebra fish may be an ideal vertebrate model system for numerous human diseases with which the genetics and biological mechanisms of the disease may be studied. Zebra fish has been successfully used in developmental genetics, and recently, neurobiologists have also started to study this species. A potentially interesting target disease amenable for analysis with zebra fish is drug addiction, e.g. alcoholism. Although genetic tools to manipulate the genome of zebra fish are available, appropriate phenotypical testing methods are often lacking. In this paper, we describe basic behavioral tests to investigate the acute effects of alcohol on zebra fish. These behavioral paradigms will be useful for the genetic and biological analysis of acute and chronic drug effects as well as addiction. In addition to presenting findings for the acute effects of alcohol, we briefly describe our strategy for generating and screening mutants. We hope that our pilot work will facilitate the future development of behavioral tests and the use of zebra fish in the genetic analysis of the biological effects of drugs of abuse.

Aggression↗
PubMed2002

An automated phylogenetic key for classifying homeoboxes.

When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.

Algorithms↗
PubMed2002

An ES-like cell line from the marine fish Sparus aurata: characterization and chimaera production.

Embryonic stem (ES) cells provide a unique tool for cell-mediated gene transfer and targeted gene mutations due to the possibility of in vitro selection of desired genotypes. When selected cells contribute to the germ line in chimaeric embryos, transgenic animals may be generated with modified genetic traits. Though the ES cell approach has up to now been limited to mice, there is an increasing interest to develop this technology in both model and commercial fish species, with so far promising results in the medaka and zebrafish. In this study, we present evidence regarding a long-term stable cell line (SaBE-1c), derived from embryonic cells of the aquaculture marine fish Sparus aurata which has been characterized for (i) cell proliferation, (ii) chromosome complement, (iii) molecular markers, and (iv) in vitro tests of pluripotency by alkaline phosphatase (AP) staining, telomerase activity, and induced cell differentiation. These cells have proved their pluripotent capacities by in vitro tests. Furthermore, we have demonstrated their ability to produce chimaeras and to contribute to the formation of tissues from all three embryonic germ layers. These features suggest that SaBE-1c cells have the potential for multiple applications for the ES technology in fish, with the added value of originating from an economically important species.

Alkaline Phosphatase↗
PubMed2002

The reaction-diffusion system: a mechanism for autonomous pattern formation in the animal skin.

How do animals acquire their various skin patterns? Although this question may seem easy, in fact it is very difficult to answer. The problem is that most animals have no related structures under the skin; therefore, the skin cells must form the patterns without the support of a prepattern. Recent progress in developmental biology has identified various molecular mechanisms that function in setting the positional information needed for the correct formation of body structure. None of these can explain how skin pattern is formed, however, because all such molecular mechanisms depend on the existing structure of the embryo. Although little is known about the underlying molecular mechanism, many theoretical studies suggest that the skin patterns of animals form through a reaction-diffusion system-a putative 'wave' of chemical reactions that can generate periodic patterns in the field. This idea had remained unaccepted for a long time, but recent findings on the skin patterns of fish have proved that such waves do exist in the animal body. In this review, we explain briefly the principles of the reaction-diffusion mechanism and summarize the recent progress made in this area.

Animals↗
PubMed2005

The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity.

We have recently described an evolutionarily conserved protein motif, designated the THAP domain, which defines a previously uncharacterized family of cellular factors (THAP proteins). The THAP domain exhibits similarities to the site-specific DNA-binding domain of Drosophila P element transposase, including a putative metal-coordinating C2CH signature (CX(2-4)CX(35-53)CX(2)H). In this article, we report a comprehensive list of approximately 100 distinct THAP proteins in model animal organisms, including human nuclear proapoptotic factors THAP1 and DAP4/THAP0, transcriptional repressor THAP7, zebrafish orthologue of cell cycle regulator E2F6, and Caenorhabditis elegans chromatin-associated protein HIM-17 and cell-cycle regulators LIN-36 and LIN-15B. In addition, we demonstrate the biochemical function of the THAP domain as a zinc-dependent sequence-specific DNA-binding domain belonging to the zinc-finger superfamily. In vitro binding-site selection allowed us to identify an 11-nucleotide consensus DNA-binding sequence specifically recognized by the THAP domain of human THAP1. Mutations of single nucleotide positions in this sequence abrogated THAP-domain binding. Experiments with the zinc chelator 1,10-o-phenanthroline revealed that the THAP domain is a zinc-dependent DNA-binding domain. Site-directed mutagenesis of single cysteine or histidine residues supported a role for the C2CH motif in zinc coordination and DNA-binding activity. The four other conserved residues (P, W, F, and P), which define the THAP consensus sequence, were also found to be required for DNA binding. Together with previous genetic data obtained in C. elegans, our results suggest that cellular THAP proteins may function as zinc-dependent sequence-specific DNA-binding factors with roles in proliferation, apoptosis, cell cycle, chromosome segregation, chromatin modification, and transcriptional regulation.

Amino Acid Motifs↗
PubMed2004

Duplication and divergence: the evolution of new genes and old ideas.

Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution. He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions. Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurrence and consequences of gene duplication, beginning in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, "transcriptomes," and "interactomes."

Animals↗
PubMed2004

Learned social preference in zebrafish.

How social aggregations arise and persist is central to our understanding of evolution, behavior, and psychology. When social groups arise within a species, evolutionary divergence and speciation can result. To understand this diversifying role of social behavior, we must examine the internal and external influences that lead to nonrandom assortment of phenotypes. Many fishes form aggregations called shoals that reduce predation risk while enhancing foraging and reproductive success. Thus, shoaling is adaptive, and signals that maintain shoals are likely to evolve under selection. Given the diversity of pigment patterns among Danio fishes, visual signals might be especially important in mediating social behaviors in this group. Our understanding of pigment pattern development in the zebrafish D. rerio allows integrative analyses of how molecular variation leads to morphological variation among individuals and how morphological variation influences social interactions. Here, we use the zebrafish pigment mutant nacre/mitfa to test roles for genetic and environmental determinants in the development of shoaling preference. We demonstrate that individuals discriminate between shoals having different pigment pattern phenotypes and that early experience determines shoaling preference. These results suggest a role for social learning in pigment pattern diversification in danios.

Animal Communication↗
PubMed2004

Variation in sequence and organization of splicing regulatory elements in vertebrate genes.

Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example, genes from the pufferfish Fugu rubripes generally contain one or more introns that are not properly spliced in mouse cells. Exploiting available genome sequence data, a battery of sequence analysis techniques was used to reach several conclusions about the organization and evolution of splicing regulatory elements in vertebrate genes. The classical splice site and putative branch site signals are completely conserved across the vertebrates studied (human, mouse, pufferfish, and zebrafish), and exonic splicing enhancers also appear broadly conserved in vertebrates. However, another class of splicing regulatory elements, the intronic splicing enhancers, appears to differ substantially between mammals and fish, with G triples (GGG) very abundant in mammalian introns but comparatively rare in fish. Conversely, short repeats of AC and GT are predicted to function as intronic splicing enhancers in fish but are not enriched in mammalian introns. Consistent with this pattern, exonic splicing enhancer-binding SR proteins are highly conserved across all vertebrates, whereas heterogeneous nuclear ribonucleoproteins, which bind many intronic sequences, vary in domain structure and even presence/absence between mammals and fish. Exploiting differences in intronic sequence composition, a statistical model was developed to predict the splicing phenotype of Fugu introns in mammalian systems and was used to engineer the spliceability of a Fugu intron in human cells by insertion of specific sequences, thereby rescuing splicing in human cells.

Animals↗
PubMed1997

Functional characterization of the trout insulin promoter: implications for fish as a favorable model of pancreas development.

The complex anatomy of the mammalian pancreas, in which the endocrine cells are grouped in islets dispersed among the predominant exocrine component, has hampered study of the molecular events governing the development of pancreatic cell lineages. To investigate whether fish may provide relevant, complementary models of pancreas development, we characterized the trout insulin (tINS) promoter and its molecular interactions with PDX1, a key transcriptional and developmental factor of the mammalian pancreas. Transfection of a luciferase reporter plasmid containing the 280 bp 5'-flanking region of the tINS gene resulted in strong activity in mammalian pancreatic beta cells but not in CHO or pituitary cells. Footprinting assays and cotransfection experiments indicated that mammalian PDX1 binds to and activates the tINS promoter. By microinjecting plasmids to fertilized zebrafish eggs, we showed that the expression of mouse PDX1 is capable of activating the co-injected tINS promoter plasmid in most cell types of the 24-h zebrafish embryo. The conserved role of PDX1 in vertebrate insulin gene regulation opens the possibility to exploit fish models in the study of pancreas development.

Animals↗
PubMed2001

Fgf/MAPK signalling is a crucial positional cue in somite boundary formation.

The temporal and spatial regulation of somitogenesis requires a molecular oscillator, the segmentation clock. Through Notch signalling, the oscillation in cells is coordinated and translated into a cyclic wave of expression of hairy-related and other genes. The wave sweeps caudorostrally through the presomitic mesoderm (PSM) and finally arrests at the future segmentation point in the anterior PSM. By experimental manipulation and analyses in zebrafish somitogenesis mutants, we have found a novel component involved in this process. We report that the level of Fgf/MAPK activation (highest in the posterior PSM) serves as a positional cue within the PSM that regulates progression of the cyclic wave and thereby governs the positions of somite boundary formation.

Animals↗
PubMed2004

Function of Cyp11a1 in animal models.

CYP11A1 encodes the P450scc enzyme that catalyzes the first and rate-limiting step of steroid biosynthesis. It is expressed in the adrenals and gonads under the control of pituitary peptide hormones. Transcription factor SF-1, which binds to the CYP11A1 promoter, plays an important role in the tissue-specific and hormonally regulated expression. Transgenic mouse experiments linking the CYP11A1 promoter to a reporter gene demonstrate the importance of the SF-1-binding site in directing balanced CYP11A1 gene expression. In addition, targeted mutagenesis of Cyp11a1 also reveals the importance of this gene in steroid secretion, gene regulation, and development of genitalia. Zebrafish cyp11a1 is expressed in the gonads and interrenal glands in the adults, similar to mammals. In addition, it is expressed in yolk syncytial layer during early embryogenesis. These two animal models complement each other for the understanding of gene regulatory pathways in human diseases related to steroid imbalance.

Animals↗
PubMed2006

Ribosomal protein gene knockdown causes developmental defects in zebrafish.

The ribosomal proteins (RPs) form the majority of cellular proteins and are mandatory for cellular growth. RP genes have been linked, either directly or indirectly, to various diseases in humans. Mutations in RP genes are also associated with tissue-specific phenotypes, suggesting a possible role in organ development during early embryogenesis. However, it is not yet known how mutations in a particular RP gene result in specific cellular changes, or how RP genes might contribute to human diseases. The development of animal models with defects in RP genes will be essential for studying these questions. In this study, we knocked down 21 RP genes in zebrafish by using morpholino antisense oligos to inhibit their translation. Of these 21, knockdown of 19 RPs resulted in the development of morphants with obvious deformities. Although mutations in RP genes, like other housekeeping genes, would be expected to result in nonspecific developmental defects with widespread phenotypes, we found that knockdown of some RP genes resulted in phenotypes specific to each gene, with varying degrees of abnormality in the brain, body trunk, eyes, and ears at about 25 hours post fertilization. We focused further on the organogenesis of the brain. Each knocked-down gene that affected the morphogenesis of the brain produced a different pattern of abnormality. Among the 7 RP genes whose knockdown produced severe brain phenotypes, 3 human orthologs are located within chromosomal regions that have been linked to brain-associated diseases, suggesting a possible involvement of RP genes in brain or neurological diseases. The RP gene knockdown system developed in this study could be a powerful tool for studying the roles of ribosomes in human diseases.

Animals↗
PubMed2006

Reverse correlation of rapid calcium signals in the zebrafish optic tectum in vivo.

Reverse correlation techniques provide a quantitative means of computing neuronal input/output relationships. Until now these methods have been limited to electrically recorded responses since unprocessed optical signals generally lack necessary temporal characteristics. We sought to overcome this barrier since combining reverse correlation with calcium imaging would afford a powerful alternative to current methods of measuring response properties of neurons non-invasively in vivo. We labeled zebrafish optic tecta with a calcium indicator and measured responses to a whole-field random flicker light stimulus. Although calcium signals exhibited slow decay kinetics, we could use computational modeling to show that the positive differential of these traces extracts high frequency information. Experimentally, we found that calcium signals processed in this way were synchronous with simultaneously measured synaptic responses and could be used with reverse correlation to determine temporal filters of neurons in the zebrafish optic tectum. These findings demonstrate that calcium responses to physiological stimulation can be processed to obtain rapid signal information and consequently to determine linear filter properties in vivo.

Animals↗