Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids. (41/144)

An evolutionary hypothesis suggested by studies of the genome of the tiger pufferfish Takifugu rubripes has now been confirmed by comparison with the genome of a close relative, the spotted green pufferfish Tetraodon nigroviridis. Ray-finned fish underwent a whole-genome duplication some 350 million years ago that might explain their evolutionary success.  (+info)

Chromosomal localization of three somatostatin genes in zebrafish. Evidence that the [Pro2]-somatostatin-14 isoform and cortistatin are encoded by orthologous genes. (42/144)

There is now evidence for the existence of two somatostatin genes in most vertebrate species, and even three somatostatin genes in teleosts. To help clarify the evolutionary relationships between the different somatostatin isoforms currently known, we characterized the somatostatin loci in a teleost species, the zebrafish Danio rerio, and compared them with the corresponding regions in the human and pufferfish genomes. The occurrence of three somatostatin genes, termed SS1, SS2 and SSII, has been previously demonstrated in the zebrafish. Radiation hybrid mapping assigned these three genes to linkage groups 15, 23 and 2, respectively. Conserved synteny of the zebrafish SS2 gene and the human cortistatin gene was revealed by comparative genomic analysis, indicating that mammalian cortistatin is orthologous to the SS2 variant of non-mammalian species. In contrast, using a similar approach, it was not possible to identify the evolutionary relationships between the atypical SSII gene of zebrafish and the other teleost SSII genes.  (+info)

The truth about mouse, human, worms and yeast. (43/144)

Genome comparisons are behind the powerful new annotation methods being developed to find all human genes, as well as genes from other genomes. Genomes are now frequently being studied in pairs to provide cross-comparison datasets. This 'Noah's Ark' approach often reveals unsuspected genes and may support the deletion of false-positive predictions. Joining mouse and human as the cross-comparison dataset for the first two mammals are: two Drosophila species, D. melanogaster and D. pseudoobscura; two sea squirts, Ciona intestinalis and Ciona savignyi; four yeast (Saccharomyces) species; two nematodes, Caenorhabditis elegans and Caenorhabditis briggsae; and two pufferfish (Takefugu rubripes and Tetraodon nigroviridis). Even genomes like yeast and C. elegans, which have been known for more than five years, are now being significantly improved. Methods developed for yeast or nematodes will now be applied to mouse and human, and soon to additional mammals such as rat and dog, to identify all the mammalian protein-coding genes. Current large disparities between human Unigene predictions (127,835 genes) and gene-scanning methods (45,000 genes) still need to be resolved. This will be the challenge during the next few years.  (+info)

Body-induced vortical flows: a common mechanism for self-corrective trimming control in boxfishes. (44/144)

Boxfishes (Teleostei: Ostraciidae) are marine fishes having rigid carapaces that vary significantly among taxa in their shapes and structural ornamentation. We showed previously that the keels of the carapace of one species of tropical boxfish, the smooth trunkfish, produce leading edge vortices (LEVs) capable of generating self-correcting trimming forces during swimming. In this paper we show that other tropical boxfishes with different carapace shapes have similar capabilities. We conducted a quantitative study of flows around the carapaces of three morphologically distinct boxfishes (spotted boxfish, scrawled cowfish and buffalo trunkfish) using stereolithographic models and three separate but interrelated analytical approaches: digital particle image velocimetry (DPIV), pressure distribution measurements, and force balance measurements. The ventral keels of all three forms produced LEVs that grew in circulation along the bodies, resembling the LEVs produced around delta-winged aircraft. These spiral vortices formed above the keels and increased in circulation as pitch angle became more positive, and formed below the keels and increased in circulation as pitch angle became more negative. Vortices also formed along the eye ridges of all boxfishes. In the spotted boxfish, which is largely trapezoidal in cross section, consistent dorsal vortex growth posterior to the eye ridge was also present. When all three boxfishes were positioned at various yaw angles, regions of strongest concentrated vorticity formed in far-field locations of the carapace compared with near-field areas, and vortex circulation was greatest posterior to the center of mass. In general, regions of localized low pressure correlated well with regions of attached, concentrated vorticity, especially around the ventral keels. Although other features of the carapace also affect flow patterns and pressure distributions in different ways, the integrated effects of the flows were consistent for all forms: they produce trimming self-correcting forces, which we measured directly using the force balance. These data together with previous work on smooth trunkfish indicate that body-induced vortical flows are a common mechanism that is probably significant for trim control in all species of tropical boxfishes.  (+info)

Molecular cloning and functional characterization of a high-affinity zinc importer (DrZIP1) from zebrafish (Danio rerio). (45/144)

Zinc is a vital micronutrient to all organisms and a potential toxicant to aquatic animals. It is therefore of importance to understand the mechanism of zinc regulation. In the present study, we molecularly cloned and functionally characterized a zinc transporter of the SLC39A family [commonly referred to as the ZIP (Zrt- and Irt-related protein) family] from the gill of zebrafish (Danio rerio) (DrZIP1). DrZIP1 protein was found to localize at the plasma membrane and to function as a zinc uptake transporter when being expressed in either chinook salmon (Oncorhynchus tshawytscha) embryonic 214 cells or Xenopus laevis oocytes. In comparison with pufferfish transporter proteins (FrZIP2 and FrECaC) that are known to facilitate cellular zinc uptake, DrZIP1 appears to have high affinity to bind and transport zinc, suggesting that it maybe a high-affinity zinc uptake transporter (Km < 0.5 microM) in fish. Orthologues of DrZIP1 were also identified in both freshwater and seawater pufferfish (Tetraodon nigroviridis and Takifugu rubripes), indicating that these proteins may be functionally conserved among different fish species. DrZIP1 mRNA is expressed in all the tissues examined in the present study and thus DrZIP1 may be a constitutive zinc uptake transporter in many cell types of zebrafish.  (+info)

The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. (46/144)

Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is phylogenetically and spatially conserved in introns that flank brain-enriched alternative exons from fish to man. Analysis of sequence from the mouse, rat, dog, chicken and pufferfish genomes revealed a strongly statistically significant association of UGCAUG with the proximal intron region downstream of brain-enriched alternative exons. The number, position and sequence context of intronic UGCAUG elements were highly conserved among mammals and in chicken, but more divergent in fish. Control datasets, including constitutive exons and non-tissue-specific alternative exons, exhibited a much lower incidence of closely linked UGCAUG elements. We propose that the high sequence specificity of the UGCAUG element, and its unique association with tissue-specific alternative exons, mark it as a critical component of splicing switch mechanism(s) designed to activate a limited repertoire of splicing events in cell type-specific patterns. We further speculate that highly conserved UGCAUG-binding protein(s) related to the recently described Fox-1 splicing factor play a critical role in mediating this specificity.  (+info)

Naturally occurring antisense: transcriptional leakage or real overlap? (47/144)

Naturally occurring antisense transcription is associated with the regulation of gene expression through a variety of biological mechanisms. Several recent genome-wide studies reported the identification of potential antisense transcripts for thousands of mammalian genes, many of them resulting from alternatively polyadenylated transcripts or heterogeneous transcription start sites. However, it is not clear whether this transcriptional plasticity is intentional, leading to regulated overlap between the transcripts, or, alternatively, represents a "leakage" of the RNA transcription machinery. To address this question through an evolutionary approach, we compared the genomic organization of genes, with or without antisense, between human, mouse, and the pufferfish Fugu rubripes. Our hypothesis was that if two neighboring genes overlap and have a sense-antisense relationship, we would expect negative selection acting on the evolutionary separation between them. We found that antisense gene pairs are twice as likely to preserve their genomic organization throughout vertebrates' evolution compared to nonantisense pairs, implying an overlap existence in the ancestral genome. In addition, we show that increasing the genomic distance between pairs of genes having a sense-antisense relationship is selected against. These findings indicate that, at least in part, the abundance of antisense transcripts observed in expressed data represents real overlap rather than transcriptional leakage. Moreover, our results imply that natural antisense transcription has considerably affected vertebrate genome evolution.  (+info)

Functional expression of a low-affinity zinc uptake transporter (FrZIP2) from pufferfish (Takifugu rubripes) in MDCK cells. (48/144)

Zinc is a vital micronutrient to all organisms and it is therefore very important to determine the mechanisms that regulate cellular zinc uptake. Previously, we reported on zinc uptake transporters from zebrafish (Danio rerio; DrZIP1) and Fugu pufferfish (Takifugu rubripes; FrZIP1) that facilitated cellular zinc uptake of high affinity (K(m)<0.5 microM) in both CHSE214 [chinook salmon (Oncorhynchus tshawytscha) embryonic 214] cells and Xenopus laevis oocytes. To investigate additional biochemical pathways of zinc uptake in fish, we molecularly cloned the second fish member (FrZIP2) of the SLC39 subfamily II from Fugu pufferfish gill. Functional characterization suggests that FrZIP2 stimulated zinc uptake in a temperature-, time-, concentration- and pH-dependent manner when overexpressed in MDCK cells (Madin-Darby canine kidney cells). In comparison with FrZIP1 and DrZIP1 (<0.5 microM), FrZIP2 appears to represent a low-affinity zinc uptake transporter (K(m)=13.6 microM) in pufferfish. FrZIP2 protein was selective for zinc, but it might also transport Cu2+, since 20 times excess of Cu2+ completely abolished its zinc uptake activity. The zinc uptake by FrZIP2 was stimulated in a slightly acidic medium (pH 5.5-6.5) and was completely blocked at pH 7.5 and above, suggesting that an inward H+ gradient might provide a driving force for zinc transport by FrZIP2. Furthermore, FrZIP2-mediated zinc uptake activity was slightly inhibited by 0.5 mM HCO3-, indicating that FrZIP2 may employ a different mechanism of zinc translocation from the assumed HCO3--coupled zinc transport used by human SLC39A2. The FrZIP2 gene was expressed in all the tissues studied herein, with especially high levels in the ovary and intestines. Thus FrZIP2 may be a prominent zinc uptake transporter of low affinity in many cell types of Fugu pufferfish.  (+info)