Neuroglobins from the zebrafish Danio rerio and the pufferfish Tetraodon nigroviridis

Neuroglobin is a recently discovered respiratory, porphyrin-containing protein that is expressed in the brain of mouse and man. Here we show that neuroglobin is also present in the teleost fish. Complete cDNA sequences are reported from the pufferfish Tetraodon nigroviridis and the zebrafish Danio rerio. In addition, the neuroglobin gene of T. nigroviridis was sequenced, demonstrating the conservation of the B12.2, E11.0 and G7.0 introns plus the presence of an additional intron in the 5' noncoding region. The fish neuroglobins each comprise 159 amino acids and are 84.3% identical. Phylogenetic analyses show a basal position of the neuroglobins within the metazoan globin tree. An enhanced amino acid substitution rate was estimated for the fish neuroglobins ( approximately 0.93 x 10(-9) amino acid substitutions per site and year) compared with their mammalian proteins ( approximately 0.39 x 10(-9) replacements per site and year).     

Karyotype and chromosome location of characteristic tandem repeats in the pufferfish Tetraodon nigroviridis

Karyotype analysis of Tetraodon nigroviridis, a pufferfish of the family Tetraodontidae with a small compact genome (385 Mb) which is currently being investigated in our laboratory, indicates that this species has 2n = 42 chromosomes. The small chromosome size (the largest pair measuring less than 3 microm) has complicated accurate chromosome pairing based on morphology alone. DAPI staining, however, provides a banding-like pattern. Because of quantitative variations of some heterochromatin classes, the chromosome formula can not be established precisely, but is estimated to include approximately 20 meta- or submetacentric chromosomes and 22 subtelocentric chromosomes. A centromeric satellite, telomeric repeats, and the major and minor rRNA clusters have been localized unequivocally by FISH. As a result, the 28S and 5S rDNA sequences can be used as chromosome-specific probes.     

Global heterochromatic colocalization of transposable elements with minisatellites in the compact genome of the pufferfish Tetraodon nigroviridis

Because of its unusual high degree of compaction and paucity of repetitive sequences, the genome of the smooth pufferfish Tetraodon nigroviridis is the subject of a well-advanced sequencing project. An astonishing diversity of transposable elements not found in the human and the mouse has been observed in the genome of T. nigroviridis. Due to the difficulty of assembling repeat-rich regions, the whole genome shotgun sequencing approach will probably fail to reveal the general organisation of this compact vertebrate genome. Therefore, in order to gain new insights into the global distribution pattern of repeated DNA in the genome of T. nigroviridis, we have reconstructed partial/complete repetitive sequences from data generated by the genome project and performed double-colour fluorescent in situ hybridization (FISH) analysis for representatives of three major categories of repeated sequences including two minisatellites (ms100 and ms104), two DNA transposons (Tol2 and Buffy1) and two non-long terminal repeat (LTR) retrotransposons (Rex3 and Babar). We show that DNA transposons and retroelements very frequently colocalize with minisatellites and mostly accumulate within heterochromatic regions. These results, which have not been reported so far for the fugu Takifugu rubripes, show that repeated elements are generally excluded from gene-rich regions in T. nigroviridis and underline the extreme degree of compartmentalization of this compact genome. The genome organization of the pufferfish is clearly different from that observed in humans, where repeated sequences make up an important fraction of euchromatic DNA, and is more similar to that observed in the fruit fly Drosophila melanogaster.     

Cloning, characterization and expression analysis of two Tetraodon nigroviridis interleukin-16 isoform genes

Interleukin-16 (IL-16) is an important pro-inflammatory cytokine that functions as a chemoattractant factor and is well characterized in human and other mammals, but is largely unknown in fish. In the present study, two isoforms of pro-IL-16 homologues were cloned and characterized from pufferfish Tetraodon nigroviridis. The full-length T. nigroviridis pro-IL-16 isoform 1 cDNA exhibits 2453 bp in size including 291 bp 5'UTR (untranslated region), 1704 bp ORF (open reading frame) and 458 bp 3'UTR, while pro-IL-16 isoform 2 cDNA exhibits a 3801 bp ORF and a 458 bp 3'UTR. Bioinformatics analysis demonstrated that the pro-IL-16 isoform 1 with a predicted mass of 60.6 kDa contained two PDZ (postsynaptic density/disc large/zona occludens-1) domains, whereas the 138.2 kDa pro-IL-16 isoform 2 had two additional PDZ domains in its N-terminal extension. RT-PCR results revealed that ,almost in all examined organs and tissues, the mRNA of both pro-IL-16 isoforms can be detected, except in intestine and gill, where the isoform 2 mRNA is absent. The two putative precursor proteins showed 30.0-33.0% identity to various mammalian and avian homologues. This is the first report of such genes in teleostean fish and we hope the molecular characterization of these two pro-IL-16 isoforms will provide insights into the study of both evolution of IL-16 precursor proteins and the immune system as a whole.     

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

We determined the whole mitochondrial genome sequence for spotted green pufferfish, Tetraodon nigroviridis (Teleostei: Tetraodontiformes). The genome (16,488 bp) contained 37 genes (two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes) plus control region as found in other vertebrates, with the gene order identical to that of typical vertebrates. The sequence was used to estimate phylogenetic relationships and divergence times among major lineages of fishes, including representative model organisms in fishes. We employed partitioned Bayesian approaches for these two analyses using two datasets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding the ND6 gene) and concatenated nucleotide sequences from the 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The resultant trees from the two datasets were well resolved and largely congruent with those from previous studies, with spotted green pufferfish being placed in a reasonable phylogenetic position. The approximate divergence times between spotted green pufferfish and model organisms in fishes were 85 million years ago (MYA) vs. torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records.     

Expression and distribution of Na, K-ATPase in gill and kidney of the spotted green pufferfish, Tetraodon nigroviridis, in response to salinity challenge

Freshwater (FW) spotted green pufferfish (Tetraodon nigroviridis) were transferred directly from a local aquarium to fresh water (FW; 0 per thousand ), brackish water (BW; 15 per thousand ), and seawater (SW; 35 per thousand ) conditions in the laboratory and reared for at least two weeks. No mortality was found. To investigate the efficient mechanisms of osmoregulation in the euryhaline teleost, distribution and expression of Na,K-ATPase (NKA) in gill and kidney of the pufferfish were examined and the osmolality, [Na+] and [Cl-] of the blood were assayed. The lowest levels of both relative protein abundance and activity were found to be exhibited in the BW group, and higher levels in the SW group than FW group. In all salinities, branchial NKA immunoreactivity was found in epithelial cells of the interlamellar region of the filament and not on the lamellae. Relative abundance of kidney NKA alpha-subunit, as well as the NKA activity, was found to be higher in the FW pufferfish than fish in BW or SW. Renal NKA appeared in the epithelial cells of distal tubules, proximal tubules, and collecting tubules, but not in glomeruli, in fish groups of various salinities. Plasma osmolality and chloride levels were significantly lower in FW pufferfish than those in BW and SW, whereas plasma sodium did not differ among the groups. Although identical distributions of NKA were found in either gill or kidney of FW-, BW- or SW-acclimated spotted green pufferfish, differential NKA expression in fish of various salinity groups was associated with physiological homeostasis (stable blood osmolality), and illustrated the impressive osmoregulatory ability of this freshwater and estuarine species in response to salinity challenge.     

Estimation of the Extent of Synteny Between Tetraodon nigroviridis and Homo sapiens Genomes

This paper presents a genomic comparison between 20 sequenced BACs (or fragments of BACs) from Tetraodon nigroviridis and the human genome. A total of 199 fish genes were identified by informatics resources, together with their putative human orthologues. Comparisons of the localizations in both species led to the identification of 32 syntenic regions and a minimum of 131 rearrangements in these regions that occurred during independent evolution of these species. This made it possible to estimate the rate of genomic rearrangements that occurred per million years (and per megabase). This rate is comparable to that obtained by comparison of the Fugu rubripes shotgun sequence data to human data but is significantly higher that those obtained by comparing the human genome to mammalian genomes. Overall, it suggests that genomic evolution by rearrangement is not uniform within the vertebrate group.Sequence data for the genomic BAC clones have been deposited with the DDBJ/EMBL/GenBank Data Libraries under accession numbers BX629360, BX629354, BX629355, BX629356, BX629357, BX629358, BX629359, and BX629360.     

Intron loss in the SART1 genes of Fugu rubripes and Tetraodon nigroviridis.

The human SART1 gene was initially identified in a screen for proteins recognised by IgE, which may be implicated in atopic disease. We have examined the genomic structure and cDNA sequence of the SART1 gene in the compact genomes of the pufferfish Fugu rubripes and Tetraodon nigroviridis. The entire coding regions of both the Fugu and Tetraodon SART1 genes are contained within single exons. The Fugu gene contains only one intron located in the 5' untranslated region. Southern blot hybridisation of Fugu genomic DNA confirmed the SART1 gene to be single copy. Partial genomic structures were also determined for the human, mouse, Drosophila and C. elegans SART1 homologues. The human and mouse genes both contain many introns in the coding region, the human gene possessing at least 20 exons. The Drosophila and C. elegans homologues contain 6 and 12 exons, respectively. This is only the second time such a difference in the organization of homologous Fugu and human genes has been reported. The Fugu and Tetraodon SART1 genes encode putative proteins of 772 and 774 aa, respectively, each having 65% amino acid identity to human SART1. Leucine zipper and basic motifs are conserved in the predicted Fugu and Tetraodon proteins.     

The role of spotted green pufferfish Tetraodon nigroviridis in controlling golden apple snail Pomacea canaliculata: an effective biological control approach involving a new agent

The golden apple snail Pomacea canaliculata is invasive in South China and poses serious harm to agricultural production and aquatic ecosystems. In the present study, we investigated the predatory potential of the spotted green pufferfish Tetraodon nigroviridis (50?mm in body length) on snails of various sizes in fresh and brackish water (4.5 ppt salinity). The survival and damage rates of 50 snails were estimated at 1, 3, 5 and 7 days. The survival rate of snails, including 10 adult snails (20–35?mm shell height), decreased less than 25% in the presence of pufferfish, and this decrease was more profound in brackish than in fresh water. Approximately 98% of the snails died in brackish water in the presence of only four pufferfish. The pufferfish also inflicted a high rate of snail injury resulting from attacks involving bites. In addition, the pufferfish affected the behaviour of the snails, with more than 95% of snails exhibiting tightly closed opercula. Thus, the results of this study suggest that pufferfish are effective for the biological control of golden apple snails.     

Cytogenetic and molecular analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes)

In view of their compact genome, pufferfish (Tetraodontiformes) have been proposed as model animal for the study of the vertebrate genome. Despite such interest, cytogenetic information about puffers is still scanty. To fill this gap, a cytogenetic analysis of T. fluviatilis has been performed using both classical and molecular techniques. C-banding, followed by DAPI staining, evidenced that in T. fluviatilis, like all other puffer species so far examined, heterochromatin is essentially AT-rich and it is located at centromeres, whereas staining with CMA₃, silver staining and FISH with a 28S ribosomal RNA gene DNA probe showed 2–4 nucleolar organizing regions (NORs) located in heterochromatic regions in the considered puffer species. FISH with the 5S probe put in evidence both in T. fluviatilis and in T. nigroviridis only a 5S cluster per haploid genome that is physically unlinked with the major ribosomal RNA genes including the 28S rRNA genes. Hybridization with the (TTAGGG)_n probe showed in all the puffers brightly fluorescent signals uniform both in size and intensity at the end of all the chromosomes. Finally, mariner-like elements (MLEs) have been identified in T. fluviatilis and they have located into the NOR-associated heterochromatin.     

Claudin-3 tight junction proteins in Tetraodon nigroviridis: cloning, tissue-specific expression, and a role in hydromineral balance

Claudins are a large family of integral transmembrane tight junction (TJ) proteins involved in regulating the permeability of the paracellular pathway. In these studies, we clone and describe the tissue distribution of four claudin-3 genes (designated Tncldn3a, Tncldn3b, Tncldn3c, and Tncldn3d) from the euryhaline spotted green puffer fish Tetraodon nigroviridis and examine the response of Tetraodon and Tncldn3 mRNAs to salinity variation (freshwater, FW; seawater, SW; and hypersaline seawater, HSW). In Tetraodon, genes encoding for claudin-3 TJ proteins are widely expressed, suggesting that claudin-3 proteins participate in regulating paracellular permeability across various epithelia within fishes. Of particular note is the widespread distribution of Tncldn3 genes in tissues that regulate hydromineral balance (gills, skin, kidney, and intestine). Renal and intestinal tissues express all four Tncldn3 genes, while the gills and skin specifically express Tncldn3a and Tncldn3c. In response to salinity variation, Tetraodon exhibits characteristics typical of a euryhaline fish species: moderate changes in blood osmolality and muscle moisture content; alterations in gill, kidney, and intestinal Na(+)-K(+)-ATPase activity; and unaltered Na(+)-K(+)-ATPase activity in the integument. In conjunction with these changes, Tncldn3 mRNA expression exhibits marked and significant salinity-dependent alterations that are both tissue and gene specific. Overall, our data suggest that a decreased abundance of claudin-3 in Tetraodon occurs in "leakier" epithelia and that claudin-3 TJ proteins will likely play an important role in the maintenance of hydromineral balance across osmoregulatory epithelia of euryhaline fishes.     

Variation of the microbiota and metabolome along the canine gastrointestinal tract

Introduction

The fecal microbiota are relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiota and metabolome at other sites along the gastrointestinal tract remains deficient.

Objective

To analyze the gastrointestinal microbiota and metabolome of healthy domestic dogs at four anatomical sites.

Methods

Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods.

Results

Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include relative concentrations of amino acids, which decreased from the small to large intestine; pyruvate, which peaked in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine.

Conclusion

The microbiota and metabolome vary significantly at different sites along the canine gastrointestinal tract.

     

Isolation and identification of novel protein kinase genes from the round-spotted pufferfish(Tetraodon fluviatilis) genomic DNA

The round-spotted pufferfishTetraodon fluviatilis has a genome size of 380 Mb which is slightly smaller than that of another pufferfish,Fugu rubripes rubripes (Fugu). Due to their compact genome and small introns, both pufferfishes have been proposed as model organisms for genome studies. In this study, we have used genomic DNA as template to perform PCR to screen for protein kinase (pk) genes. Forty-oneT. fluviatilis pk genes encoding 7 receptor tyrosine kinases, 14 nonreceptor tyrosine kinases, 16 serine/threonine kinases, 1 dual kinase and 3 novel kinases have been identified. The success of this approach depends on the size and location of the introns. Most of the identifiedpk gene fragments contain introns, ranging from 71 to 300 bp, with an average of 120 bp. It is noteworthy that the intron/exon boundaries of certain genes which belong to the same family are identical. We also analyzed by specific RT-PCR primers the expression profile of those 3 novel genes as well as some selectedpk genes in a variety of tissues. We found thaterbB3,pku , mrk, CaMK I,CaMKII, and two novel kinase genes (133 and 3–26) are expressed in all tissues examined. However, the novel clone 146 is strongly expressed in the brain and weakly in the intestine, kidney and heart.     

Cellular distribution of prostanoid EP receptors mRNA in the rat gastrointestinal tract

The inhibition of PGE(2) synthesis resulting from sustained NSAIDs therapy has been linked to gastrointestinal irritations and ulceration. The multiple physiological effects of PGE(2) in the gut are mediated through the activation of four receptors termed EP(1-4). The aim of the study was to determine the precise distribution of the four prostaglandin E(2) receptors in the rat stomach, small intestine, and colon. We used non-radioactive in situ hybridization techniques on paraffin-embedded tissue. Mucous cells of the stomach and goblet cells of the small intestine and colon were found to express mRNA for all four EP subtypes. A positive hybridization signal for EP(1), EP(3), and EP(4) was detected in the parietal cells of the stomach whereas the chief cells expressed low levels of EP(1) and EP(3). The EP(1) and EP(3) receptor mRNA could also be detected in the muscularis mucosa, longitudinal muscle and enteric ganglias of the stomach and small intestine. However, close examination of the enteric ganglias indicated that most of the positive labeling was localized to the glial cells, although some neurons did express EP(3). In conclusion, we have detailed the distribution of prostanoid EP receptors in the gut at the cellular level, giving new insights to the role of prostaglandins in gastrointestinal functions.