| molecular cloning of a novel lipocalin-1 interacting human cell membrane receptor using phage display. | human lipocalin-1 (lcn-1, also called tear lipocalin), a member of the lipocalin structural superfamily, is produced by a number of glands and tissues and is known to bind an unusually large array of hydrophobic ligands. apart from its specific function in stabilizing the lipid film of human tear fluid, it is suggested to act as a physiological scavenger of potentially harmful lipophilic compounds, in general. to characterize proteins involved in the reception, detoxification, or degradation of ... | 2001 | 11287427 |
| are all fishes ancient polyploids? | euteleost fishes seem to have more copies of many genes than their tetrapod relatives. three different mechanisms could explain the origin of these 'extra' fish genes. the duplicates may have been produced during a fish-specific genome duplication event. a second explanation is an increased rate of independent gene duplications in fish. a third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. these three hypothe ... | 2003 | 12836686 |
| genomic structure and evolutionary conservation of the tyrosinase gene family from fugu. | the tyrosinase gene family encompasses three members, tyrosinase, tyrosinase-related protein 1 (tyrp1) and dopachrome tautomerase (dct), which encode for proteins implicated in melanin synthesis. in human and mouse, genomic organization is known for all three genes, revealing common features of regulatory elements and of exon/intron structure. we have set out to identify the complete family from a more primitive vertebrate, the pufferfish fugu (takifugu rubripes), which is characterized by a com ... | 2002 | 12039032 |
| identification of tetrodotoxin and fish species in a dried dressed fish fillet implicated in food poisoning. | there were five victims of neurotoxic food poisoning from a dried dressed fish fillet in changhua county, taiwan, in february 2000. the toxicity of the dried dressed fish fillets was 243 mouse units per g according to a tetrodotoxin bioassay. the partially purified toxin was identified as tetrodotoxin and anhydrotetrodotoxin. the sequence of the 376-nucleotide region in the cytochrome b gene of the mitochondrial dna exhibited the same genotype as that of the toxic puffer fish lagocephalus lunari ... | 2002 | 11848573 |
| impacts of diclidophorid monogenean infections on fisheries in japan. | many monogeneans are pathogenic to economically important fish in japan. however no other monogenean is comparable with the diclidophorids, heterobothrium okamotoi and neoheterobothrium hirame, on the scale of impacts they inflict on japanese fisheries. the shared importance of the two monogenean infections lies in their pathogenicity, fecundity and tolerance to chemical treatment. heterobothrium okamotoi infects the gills and wall of the branchial cavity of the tiger puffer, takifugu rubripes ( ... | 2002 | 11835977 |
| molecular cloning and sequencing of japanese pufferfish (takifugu rubripes) nadph oxidase cdnas. | the superoxide-producing nadph oxidase complex of phagocytes plays a crucial role in host defenses against microbial infection. nadph oxidase consists of a membrane heterodimeric protein, composed of gp91phox and p22phox, and cytosolic proteins, p40phox, p47phox and p67phox. in the present study, cdnas of all the components of nadph oxidase were cloned from peripheral white blood cells of the japanese pufferfish utilizing the reverse transcription-polymerase chain reaction. the sequences of thes ... | 2004 | 15183032 |
| cytosine methylation and cpg, tpg (cpa) and tpa frequencies. | an analysis of dinucleotide frequencies was carried out on dnas from insects and mammals, as well as on large dna sequences from the genomes of drosophila melanogaster, anopheles gambiae, puffer fish (takifugu rubripes), zebra fish (danio rerio) and human. these organisms were chosen because drosophila and anopheles dnas have an extremely low level of methylation, human dna a high level and fish dna a two-fold higher level compared to human. the results indicate that: (i) cpg deficiency and the ... | 2004 | 15177689 |
| [toxicity of puffer fish cultured in netcages]. | during 1990 to 2003, the toxicity of the liver in 4,515 specimens of the puffer fish takifugu rubripes (torafugu) cultured in netcages or on land were investigated by means of mouse bioassay and liquid chromatography-mass spectrometry (lc/ms). other tissues (skin, muscles, gonads, etc.) were also investigated in some of them. all the livers and other parts examined were found to be non-toxic. the peak corresponding to tetrodotoxin (ttx) was not detected in the samples by lc/ms analysis for ttx ( ... | 2004 | 15468934 |
| identification and comparative analysis of the rpl14 gene from takifugu rubripes. | the ribosomal protein rpl14 gene has been characterized in several species, including, human, rat and fruit fly. haploinsufficiency for the gene causes the minute phenotype in drosophila, and it has been proposed as a regulator in the tumorigenic pathway in human. several features concerning the gene structure have been studied, and some of these differ between human/rat and drosophila. to address functional and evolutionary questions about these differences we have isolated and sequenced a cdna ... | 2003 | 15061815 |
| an enigmatic fourth runt domain gene in the fugu genome: ancestral gene loss versus accelerated evolution. | the runt domain transcription factors are key regulators of developmental processes in bilaterians, involved both in cell proliferation and differentiation, and their disruption usually leads to disease. three runt domain genes have been described in each vertebrate genome (the runx gene family), but only one in other chordates. therefore, the common ancestor of vertebrates has been thought to have had a single runt domain gene. | 2004 | 15527507 |
| comparative analysis of two slc11 (nramp) loci in takifugu rubripes. | to study the evolution of the solute carrier family 11 (slc11; formerly nramp) protein, we isolated and characterized two paralogs from the pufferfish takifugu rubripes (fugu). these teleost genes, designated fugu slc11a-a and fugu slc11a-b, comprise open reading frames of 1743 nucleotides (581 amino acids) and 1662 nt (554 aa), respectively. the proteins are 81% similar, and both exhibit signature features of the slc11 family of proteins including 12 transmembrane domains, a conserved transport ... | 2004 | 14965472 |
| vertebrate 2xrbd hnrnp proteins: a comparative analysis of genome, mrna and protein sequences. | hnrnp proteins are involved in many cell functions, primarily in pre-mrna processing. we report here a comparative analysis of the genes of the 2xrbd members of the hnrnp family and of their expression products. starting from the seven well characterized hnrnp members of human and murine origin (a0, a1, a2/b1, a3, ab, d and dl) and the three musashi-like proteins with related rbd tandems (msi1, msi2 and dazap1), we identified through blast search 12 homologous genes in the genome of danio rerio ... | 2005 | 15680582 |
| molecular cloning and functional characterization of a high-affinity zinc importer (drzip1) from zebrafish (danio rerio). | 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 ... | 2005 | 15683366 |
| evolution of the relaxin-like peptide family. | the relaxin-like peptide family belongs in the insulin superfamily and consists of 7 peptides of high structural but low sequence similarity; relaxin-1, 2 and 3, and the insulin-like (insl) peptides, insl3, insl4, insl5 and insl6. the functions of relaxin-3, insl4, insl5, insl6 remain uncharacterised. the evolution of this family has been contentious; high sequence variability is seen between closely related species, while distantly related species show high similarity; an invertebrate relaxin s ... | 2005 | 15707501 |
| evolution of vertebrate e protein transcription factors: comparative analysis of the e protein gene family in takifugu rubripes and humans. | e proteins are essential for b lymphocyte development and function, including immunoglobulin (ig) gene rearrangement and expression. previous studies of b cells in the channel catfish (ictalurus punctatus) identified e protein homologs that are capable of binding the mue5 motif and driving a strong transcriptional response. there are three e protein genes in mammals, heb (tcf12), e2a (tcf3), and e2-2 (tcf4). the major expressed e proteins found in catfish b cells are homologs of heb and of e2a. ... | 2005 | 15713784 |
| the repertoire of trace amine g-protein-coupled receptors: large expansion in zebrafish. | trace amines, such as tyramine, beta-phenylethylamine, tryptamine, and octopamine, are present in trace levels in nervous systems and bind a specific family of g-protein-coupled receptors (gpcr), but the function or origin of this system is not well understood. we searched the genomes of several eukaryotic species for receptors similar to the mammalian trace amine (ta) receptor subfamily. we identified 18 new receptors in rodents that are orthologous to the previously known ta-receptors. remarka ... | 2005 | 15804416 |
| major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates. | it has been suggested that fish have more genes than humans. whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. we analyzed the complete genome of the pufferfish takifugu rubripes (fugu) and compared it with the paranome of humans. we show that most paralogous genes of fugu are the result of three complete genome duplicatio ... | 2004 | 14757817 |
| developmental roles of pufferfish hox clusters and genome evolution in ray-fin fish. | the pufferfish skeleton lacks ribs and pelvic fins, and has fused bones in the cranium and jaw. it has been hypothesized that this secondarily simplified pufferfish morphology is due to reduced complexity of the pufferfish hox complexes. to test this hypothesis, we determined the genomic structure of hox clusters in the southern pufferfish spheroides nephelus and interrogated genomic databases for the japanese pufferfish takifugu rubripes (fugu). both species have at least seven hox clusters, in ... | 2004 | 14707165 |
| the melanocortin system in fugu: determination of pomc/agrp/mcr gene repertoire and synteny, as well as pharmacology and anatomical distribution of the mcrs. | the g-protein-coupled melanocortin receptors (mcrs) play an important role in a variety of essential functions such as the regulation of pigmentation, energy homeostasis, and steroid production. we performed a comprehensive characterization of the mc system in fugu (takifugu rubripes). we show that fugu has an agrp gene with high degree of conservation in the c-terminal region in addition to a pomc gene lacking gamma-msh. the fugu genome contains single copies of four mcrs, whereas the mc3r is m ... | 2004 | 14694081 |
| unusual genomic structure: melanocortin receptors in fugu. | the melanocortin (mc) receptors are found in five subtypes in mammals and chicken, while recent studies have shown that the fugu (takifugu rubripes) genome has only four mc receptors and the zebrafish genome has six subtypes. the mc3 receptor seems to be missing from the two closely related pufferfishes, fugu and tetraodon (tetraodon nigroviridis). the mc2 and mc5 receptors in the pufferfish have introns. moreover, these two receptors are found in a tandem that is remarkably conserved in several ... | 2005 | 15891089 |
| functional expression of a low-affinity zinc uptake transporter (frzip2) from pufferfish (takifugu rubripes) in mdck cells. | 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 biochemica ... | 2005 | 15907194 |
| identification and characterization of two parathyroid hormone-like molecules in zebrafish. | zebrafish (danio rerio) have receptors homologous to the human pth (hpth)/pthrp receptor (pth1r) and pth-2 receptor (pth2r) and an additional receptor (pth3r) with high homology to the pth1r. to find natural ligands for zpth1r and zpth3r, we searched the zebrafish genomic database and discovered two distinct regions that, when translated (zpth1 and zpth2), showed high homology to hpth. isolation of cdnas and determination of the intron/exon boundaries revealed genomic structures which were simil ... | 2004 | 14684608 |
| molecular diversity of skin mucus lectins in fish. | among lectins in the skin mucus of fish, primary structures of four different types of lectin have been determined. congerin from the conger eel conger myriaster and ajl-1 from the japanese eel anguilla japonica were identified as galectin, characterized by its specific binding to beta-galactoside. eel has additionally a unique lectin, ajl-2, which has a highly conserved sequence of c-type lectins but displays ca(2+)-independent activity. this is rational because the lectin exerts its function o ... | 2003 | 14662297 |
| characterization of hey bhlh genes in teleost fish. | hairy-related basic helix-loop-helix (bhlh) transcription factors are targets of delta-notch signaling and represent essential components for a number of cell fate decisions during vertebrate embryogenesis. hey genes encode a subfamily of hairy-related proteins that have been implicated in processes like somitogenesis, blood vessel and heart development. we have identified and characterized hey genes in three teleost fish lineages using degenerate pcr and database searches. phylogenetic analysis ... | 2003 | 14593478 |
| molecular cloning of the bcl-6 gene, a transcriptional repressor for b-cell differentiation, in torafugu (takifugu rubripes). | b-cell lymphoma-6 (bcl-6) is a transcriptional repressor that prevents the terminal differentiation of mature b-cells to plasma cells, and is essential for germinal center formation in the primary lymphoid organs of mammals. in this study, we identified the bcl-6 gene in torafugu (takifugu rubripes) using the torafugu genome database, and analyzed the expression of bcl-6 mrna in various tissues of torafugu, using rt-pcr. the bcl-6 gene consisted of eight exons and seven introns spanning a genome ... | 2006 | 16076494 |
| structure and evolution of the teleost extraretinal rod-like opsin (errlo) and ocular rod opsin (rho) genes: is teleost rho a retrogene? | in teleost fish examined to date the ocular rod opsin gene, rho, is intronless, unlike the rod opsin genes of other vertebrate classes which possess a five exon/four intron structure. we have examined in silico the structure of rho (which is expressed uniquely in the retina) and the closely related extraretinal rod-like opsin (exo-rhodopsin) gene, errlo (which is expressed uniquely in the pineal), in the puffer-fish, fugu rubripes (takifugu rubripes). whilst the ocular rho is intronless in commo ... | 2003 | 13677319 |
| susceptibility of cultured juveniles of several marine fish to the sevenband grouper nervous necrosis virus. | piscine nodaviruses (betanodaviruses) have been tentatively divided into four genotypes (sjnnv, rgnnv, tpnnv and bfnnv) and it is suggested that host specificity is different among these genotypes. in the present study, a betanodavirus [sevenband grouper nervous necrosis virus (sgnnv)] belonging to the redspotted grouper nervous necrosis virus (rgnnv) genotype, to which most betanodaviruses from warm water fish are identified, was evaluated for its pathogenicity to hatchery-reared juveniles of s ... | 2003 | 12962219 |
| molecular evolutionary analysis of the widespread piggybac transposon family and related "domesticated" sequences. | piggybac is a short inverted-repeat-type dna transposable element originally isolated from the genome of the moth trichoplusia ni. it is currently the gene vector of choice for the transformation of various insect species. a few sequences with similarity to piggybac have previously been identified from organisms such as humans ( looper), the pufferfish takifugu rubripes ( pigibaku), xenopus ( tx), daphnia ( pokey), and the oriental fruit fly bactrocera dorsalis. we have now identified 50 piggyba ... | 2003 | 12955498 |
| identification of nogo-66 receptor (ngr) and homologous genes in fish. | the nogo-66 receptor ngr has been implicated in the mediation of inhibitory effects of central nervous system (cns) myelin on axon growth in the adult mammalian cns. ngr binds to several myelin-associated ligands (nogo-66, myelin associated glycoprotein, and oligodendrocyte-myelin glycoprotein), which, among other inhibitory proteins, impair axonal regeneration in the cns of adult mammals. in contrast to mammals, severed axons readily regenerate in the fish cns. nevertheless, fish axons are repe ... | 2004 | 12949137 |
| identification and characterization of the dna-binding properties of a zhangfei homologue in japanese pufferfish, takifugu rubripes. | zhangfei is a basic region-leucine zipper (bzip) transcription factor identified through its interaction with a herpesvirus-related host cell factor hcf1 (c1). unlike most bzip proteins, the mammalian zhangfei protein does not bind dna as homodimers. it is believed due to the absence of an asparagine residue in the basic region, which forms the dna-recognition motif, nxxaaxxcr, in all bzip proteins. here, we report the identification and characterization of a novel zhangfei homologue in takifugu ... | 2006 | 16352292 |
| strong conservation of the human nf2 locus based on sequence comparison in five species. | we analyzed 137 kb covering human neurofibromatosis 2 ( nf2) tumor suppressor locus and orthologous loci from baboon, mouse, rat, and pufferfish takifugu rubripes. a predominant feature of human-rodent conservation is a very similar distribution of conserved islands, regarding length, position, and degree of identity. by use of a threshold of 75% identity over > or =100 bp of gap-free alignment, comparisons of human-mouse sequences resulted in 3.58% for extra-exonic conservation, which can be co ... | 2003 | 12925885 |
| genome mapping of the orange blotch colour pattern in cichlid fishes. | the dramatic variation of cichlid fish colour pattern is thought to function in mate choice, evolve by sexual selection, and contribute to explosive speciation. here, we combine linkage mapping and population genetic analyses to identify a single region of the cichlid genome responsible for the orange blotch (ob) colour phenotype. in each analysis, ob is tightly linked to the c-ski1 gene. additionally, we use comparative mapping information from the takifugu rubripes and human genomes to suggest ... | 2003 | 12919484 |
| four functionally distinct c-type natriuretic peptides found in fish reveal evolutionary history of the natriuretic peptide system. | natriuretic peptides (nps) are major cardiovascular and osmoregulatory hormones in vertebrates. although tetrapods generally have three subtypes, atrial np (anp), b-type np (bnp), and c-type np (cnp), some teleosts lack bnp, and sharks and hagfish have only one np. thus, nps have diverged during fish evolution, possibly reflecting changes in osmoregulatory systems. in this study, we found, by cdna cloning, four distinct cnps (1 through 4) in the medaka (oryzias latipes) and puffer fish (takifugu ... | 2003 | 12893874 |
| regulatory roles of conserved intergenic domains in vertebrate dlx bigene clusters. | dlx homeobox genes of vertebrates are generally arranged as three bigene clusters on distinct chromosomes. the dlx1/dlx2, dlx5/dlx6, and dlx3/dlx7 clusters likely originate from duplications of an ancestral dlx gene pair. overlaps in expression are often observed between genes from the different clusters. to determine if the overlaps are a result of the conservation of enhancer sequences between paralogous clusters, we compared the dlx1/2 and the dlx5/dlx6 intergenic regions from human, mouse, z ... | 2003 | 12670995 |
| carbohydrate-binding site of a novel mannose-specific lectin from fugu (takifugu rubripes) skin mucus. | pufflectin-s, identified in the skin mucus of the fugu takifugu rubripes, is a novel mannose-specific lectin with similar structure to monocotyledonous plant lectins. in the present study, mutational analysis was used to reveal the mannose-binding sites of pufflectin-s. putative binding sites were mutated as follows: binding site 1; rpl-d32e (asp32-->glu32), rpl-n34s (asn34-->ser34) and rpl-v36a (val36-->ala36) whereas binding site 2; rpl-d61e (asp61-->glu61), rpl-n63s (asn63-->ser63) and rpl-v6 ... | 2006 | 16488640 |
| comparative analysis of vertebrate shh genes identifies novel conserved non-coding sequence. | the puffer fish takifugu rubripes (fugu), with its compact genome, is an ideal model organism for comparative genomics. sonic hedgehog (shh) is a key protein in the patterning of differentiating cells during embryonic development. we have sequenced the fugu shh gene and compared it with the mammalian and zebrafish orthologs, identifying a number of novel conserved, non-coding sequences upstream of exon one and within the two introns. additional conserved sequences serve to delineate activator re ... | 2003 | 12647242 |
| genome duplication, a trait shared by 22000 species of ray-finned fish. | through phylogeny reconstruction we identified 49 genes with a single copy in man, mouse, and chicken, one or two copies in the tetraploid frog xenopus laevis, and two copies in zebrafish (danio rerio). for 22 of these genes, both zebrafish duplicates had orthologs in the pufferfish (takifugu rubripes). for another 20 of these genes, we found only one pufferfish ortholog but in each case it was more closely related to one of the zebrafish duplicates than to the other. forty-three pairs of duplic ... | 2003 | 12618368 |
| a multispecies comparison of the metazoan 3'-processing downstream elements and the cstf-64 rna recognition motif. | the cleavage stimulation factor (cstf) is a required protein complex for eukaryotic mrna 3'-processing. cstf interacts with 3'-processing downstream elements (dses) through its 64-kda subunit, cstf-64; however, the exact nature of this interaction has remained unclear. we used est-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mrna from ten metazoan species, including homo sapiens, canis familiaris, rattus norvegicus, mus musculus, gallus gallus, dani ... | 2006 | 16542450 |
| molecular cloning of the pufferfish (takifugu rubripes) mx gene and functional characterization of its promoter. | mx proteins are members of a family of interferon-inducible genes that are expressed by cells in response to viral infection. they are important determinants of innate immunity against viral infection in vertebrates. we cloned the pufferfish ( takifugu rubripes) mx gene and sequenced 80 kb from the mx locus. the fugu mx gene spans 3.4 kb from the transcription start site to the polyadenylation signal, and is made up of 12 exons and 11 introns. the protein sequence encoded by the fugu mx gene is ... | 2003 | 12557057 |
| pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish. | we used phylogenetic analyses of protein families containing two or more pairs of orthologues in the genomes of human and pufferfish (takifugu rubripes) to test the hypothesis that these sequences show a strong signal of polyploidization events hypothesized to have occurred early in vertebrate history. in order to test for evidence of two distinct rounds of polyploidization (the 2r hypothesis), we compared the pattern of amino acid sequence divergence of proteins encoded by genes duplicated just ... | 2004 | 15186818 |
| the granulocyte colony-stimulating factors (csf3s) of fish and chicken. | granulocyte colony-stimulating factor (csf3) is a glycoprotein cytokine, which influences the hematopoiesis of the phagocytic neutrophils and its precursors and was used extensively in cancer therapy and for the treatment of neutropenia in mammals. however, csf3 is yet to be identified in nonmammalian species mainly because of its rapid mutation. here, we report the first csf3 genes from three teleost fishes: japanese flounder (paralichthys olivaceus), fugu (takifugu rubripes), and green-spotted ... | 2006 | 16738939 |
| molecular cloning and characterisation of sea bass (dicentrarchus labrax l.) caspase-3 gene. | caspase-3 is one of the major caspases operating in apoptosis, cleaving and inactivating a number of molecules and largely contributing to the apoptotic phenotype and the dismantling of the apoptoting cell. the opening reading frame of sea bass (dicentrarchus labrax l.) caspase-3 has 281 amino acids. the complete sequence of caspase-3 shows a very close homology to the correspondent sequence from other vertebrates, in particularly with that of takifugu rubripes and oryzias latipes, with 87.7 and ... | 2007 | 16780952 |
| structural phylogenetic analysis of activation-induced deaminase function. | in mammals, activation-induced deaminase (aid) initiates somatic hypermutation (shm) and class switch recombination (csr) of ig genes. shm and csr activities require separate regions within aid. a chromosome region maintenance 1 (crm1)-dependent nuclear export signal (nes) at the aid c terminus is necessary for csr, and has been suggested to associate with csr-specific cofactors. csr appeared late in aid evolution, during the emergence of land vertebrates from bony fish, which only display shm. ... | 2006 | 16785531 |
| the flounder organic anion transporter foat has sequence, function, and substrate specificity similarity to both mammalian oat1 and oat3. | the flounder renal organic anion transporter (foat) has substantial sequence homology to mammalian basolateral organic anion transporter orthologs (oat1/oat1 and oat3/oat3), suggesting that foat may have functional properties of both mammalian forms. we therefore compared uptake of various substrates by rat oat1 and oat3 and human oat1 and oat3 with the foat clone expressed in xenopus oocytes. these data confirm that estrone sulfate is an excellent substrate for mammalian oat3/oat3 transporters ... | 2006 | 16857889 |
| en bloc duplications, mutation rates, and densities of amino acid changes clarify the evolution of vertebrate alpha-1,3/4-fucosyltransferases. | numerous vertebrates have four alpha-1,3/4-fucosyltransferase genes (fut9, fut7, fut4, and fut lewis) belonging to the same family. until now, studies on the evolution of this family have mainly focused on lewis genes but how the other alpha-1,3/4-fucosyltransferases have emerged from a common ancestor is not well known. in order to define the respective roles of duplications and mutations, we have compared amino acid sequences representative of bony fish (takifugu rubripes), amphibians (xenopus ... | 2006 | 16927008 |
| identification and characterization of the zebrafish and fugu genes encoding tuberoinfundibular peptide 39. | although the pth type 2 receptor (pth2r) has been isolated from mammals and zebrafish, only its mammalian agonist, tuberoinfundibular peptide 39 (tip39), has been characterized thus far. to determine whether zebrafish tip39 (ztip39) functions similarly with the zebrafish pthr (zpth2r) and human pth2rs and to determine its tissue-specific expression, fugu (takifugu rubripes) and zebrafish (danio rerio) genomic databases were screened with human tip39 (htip39) sequences. a single tip39 gene was id ... | 2004 | 15297442 |
| molecular cloning and expression analysis of a macrophage-colony stimulating factor receptor-like gene from rainbow trout, oncorhynchus mykiss. | the m-csf and its receptor (m-csfr, csf-1r or c-fms proto-oncogene) system were initially implicated as essential in mammals for normal monocyte development as well as for pregnancy. to allow a comparison with the m-csf and m-csfr system of an oviparous animal, we cloned a m-csfr-like gene from rainbow trout (oncorhynchus mykiss). the gene was cloned from a cdna library of head kidney. it contained an open reading frame encoding 967 amino acids with a predicted size of 109 kda. the putative amin ... | 2005 | 15488938 |
| inparanoid: a comprehensive database of eukaryotic orthologs. | the inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; anopheles gambiae, caenorhabditis briggsae, caenorhabditis elegans, drosophila melanogaster, danio rerio, takifugu rubripes, gallus gallus, homo sapiens, mus musculus, pan troglodytes, rattus norvegicus, oryza sativa, plasmodium falciparum, arabidopsis thaliana, escherichia coli, saccharomyces cerevisiae and schizosaccharomyces pombe. complete proteomes ... | 2005 | 15608241 |
| identification of cdna coding for a homologue to mammalian leptin from pufferfish, takifugu rubripes. | we identified cdna coding for a homologue to mammalian leptin in puffer, takifugu rubripes, using genomic synteny around the human leptin gene. in addition to significant sequence homologies, the puffer leptin (plep) displays characteristic structural features in common with mammalian leptin. the plep mrna was expressed mostly in the liver that contained abundant lipids. in addition, homologues to plep were found in the databanks for three fish species (salmon, medaka, and tetraodon) and two amp ... | 2005 | 15808904 |
| characterization and tissue distribution of multiple agouti-family genes in pufferfish, takifugu rubripes. | four types of agouti-family genes (agrp1, agrp2, asip1 and asip2) were obtained from torafugu, takifugu rubripes. their characterization and structure were analyzed to elucidate the relationship among the torafugu agouti-family genes. both agrp1 and agrp2 showed genomic synteny with the human agrp gene. phylogenetic tree analysis showed that agrp1 formed a cluster with human agrp. we inferred that torafugu agrp1 and agrp2 are orthologs of human agrp and that they are paralogous genes derived fro ... | 2006 | 17097766 |
| in vivo characterization of a vertebrate ultraconserved enhancer. | genomic sequence comparisons among human, mouse, and pufferfish (takifugu rubripes (fugu)) have revealed a set of extremely conserved noncoding sequences. while this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change to retain in vivo functionality, such elements have been minimally explored experimentally. in this study, we describe the in-depth characterization of an ancient conserved enhancer, dc2, located near the dachshund ... | 2005 | 15885503 |
| agouti-related proteins (agrps) and agouti-signaling peptide (asip) in fish and chicken. | we performed an intensive search on sequence databases to identify orthologues of asip and agrp peptides in a number of different species, revealing a number of genomic fragments coding for the c-terminal part of agouti-related motifs, different from annotated peptide sequences, including one fragment from chicken, two from zebrafish, two from fugu (takifugu rubripes), and three from tetraodon (tetraodon nigroviridis). we have thus shown for the first time that both agrp and asip genes exist in ... | 2005 | 15891063 |
| the evolution of vertebrate toll-like receptors. | the complete sequences of takifugu toll-like receptor (tlr) loci and gene predictions from many draft genomes enable comprehensive molecular phylogenetic analysis. strong selective pressure for recognition of and response to pathogen-associated molecular patterns has maintained a largely unchanging tlr recognition in all vertebrates. there are six major families of vertebrate tlrs. this repertoire is distinct from that of invertebrates. tlrs within a family recognize a general class of pathogen- ... | 2005 | 15976025 |
| interphotoreceptor retinoid-binding protein gene structure in tetrapods and teleost fish. | the interphotoreceptor retinoid-binding protein (irbp) gene possesses an unusual structure, encoding multiple repeats, each consisting of about 300 amino acids. our goals were to gain insight into the function of irbp, and to test the current model for the evolution of irbp, in which repeats were replicated from a simpler ancestral gene. | 2006 | 17200656 |
| ammonia secretion from fish gill depends on a set of rh glycoproteins. | ammonia excretion from the gill in teleost fish is essential for nitrogen elimination. although numerous physiological studies have measured ammonia excretion, the mechanism of ammonia movement through the membranes of gill epithelial cells is still unknown. mammalian rh glycoproteins are members of a family of proteins that mediate ammonia transport in bacteria, yeast, and plants. we identified the rh glycoprotein homologs, frhag, frhbg, frhcg1, and frhcg2, of the pufferfish, takifugu rubripes. ... | 2007 | 17218543 |
| striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences. | in a recent study, 1373 highly conserved non-coding elements (cnes) were detected by aligning the human and takifugu rubripes (fugu) genomes. the remarkable degree of sequence conservation in cnes compared with their surroundings suggested comparing the base composition within cnes with their 5' and 3' flanking regions. the analysis reveals a novel, sharp and distinct signal of nucleotide frequency bias precisely at the border between cnes and flanking regions. | 2005 | 15979195 |
| two interleukin (il)-15 homologues in fish from two distinct origins. | here, we report two distinct genes in teleosts that are homologous to interleukin (il)-15. the two genes, isolated from fugu (takifugu rubripes), resemble to mammalian il-15 but differ from il-2 and il-21 in their amino acid sequences, the possessing of an extraordinary long signal peptide and more widespread tissue localization. in addition, multiple out-of-frame aug codons, the negative translational regulators of mammalian il-15 genes were also detected in the 5'-utr of the two genes. fugu il ... | 2006 | 16055191 |
| subfunctionalization of expression and peptide domains following the ancient duplication of the proopiomelanocortin gene in teleost fishes. | the proopiomelanocortin gene (pomc) encodes several bioactive peptides, including adrenocorticotropin hormone, alpha-, beta-, and gamma-melanocyte-stimulating hormone, and the opioid peptide beta-endorphin, which play key roles in vertebrate physiology. in the human, mouse, and chicken genomes, there is only one pomc gene. by searching public genome projects, we have found that tetraodon (tetraodon nigroviridis), fugu (takifugu rubripes), and zebrafish (danio rerio) possess two pomc genes, which ... | 2005 | 16093565 |
| structural analysis of cdnas coding for 4snc-tudor domain protein from fish and their expression in yellowtail organs. | we cloned complementary dnas for 4snc-tudor protein (sn4tdr) from yellowtail (seriola quinqueradiata), torafugu (takifugu rubripes), and zebrafish (danio rerio). this protein contains 4 staphylococcal nuclease domains at the n terminus followed by a tudor domain. we also identified the 4snc-tudor proteins highly homologous to that in yellowtail from the takifugu genomic database. according to the smart database, these fish proteins had an overlapping tudor domain (smart00333) with a complete 5 s ... | 2005 | 16132464 |
| mucus ph of the tiger puffer takifugu rubripes is an important factor for host identification by the monogenean heterobothrium okamotoi. | we examined a host-finding factor of the monogenean heterobothrium okamotoi oncomiracidia to develop an alternative prophylaxis. h. okamotoi oncomiracidia attached preferentially to gill filaments and skin mucus from the tiger puffer takifugu rubripes compared with corresponding material from other tested fishes (amber jack seriola dumerili, red sea bream pagrus major, japanese flounder paralichthys olivaceus and spotted halibut verasper variegatus). the body mucus ph of the tiger puffer was 6.4 ... | 2003 | 12964825 |
| ligand-dependent transcriptional activities of four torafugu pufferfish takifugu rubripes peroxisome proliferator-activated receptors. | structural and functional properties were investigated for four peroxisome proliferator-activated receptors (ppars), pparalpha1, pparalpha2, pparbeta, and ppargamma, from torafugu pufferfish takifugu rubripes and determined for their transcriptional activity by the reporter assay using reporter plasmids containing three copies of the acyl-coa oxidase ppar response element. although torafugu ppars showed a high similarity in the primary structure to other vertebrate counterparts, torafugu pparalp ... | 2007 | 17632107 |
| co-evolutionary analysis of insulin/insulin like growth factor 1 signal pathway in vertebrate species. | insulin/insulin like growth factor 1 signaling pathway plays an essential role on the regulation of variant, interrelated and fundamental processes, such as metabolism, growth, reproduction and aging. this pathway is highly conserved during evolution. we analyzed eight vertebrate species' insulin/insulin like growth factor 1 pathway and examined the co-evolutionary relationship between different protein components by quantifying similarity of phylogenetic trees. the collected species include tak ... | 2006 | 16146739 |
| identification, cloning and characterization of a plasma membrane zinc efflux transporter, trznt-1, from fugu pufferfish (takifugu rubripes). | an orthologue of the mammalian znt-1 (zinc transporter-1) gene was cloned from the intestine of the torafugu pufferfish (takifugu rubripes), demonstrating that this gene predates the evolution of land-living vertebrates. trznt-1 (t. rubripes znt-1) shares overall topology with other members of the znt-1 family of zinc transporters, with six tms (transmembrane domains) including a large histidine-rich intracellular loop between tm iv and v and intracellular c- and n-termini. expression of trznt-1 ... | 2006 | 16212555 |
| evolutionary origins of the endocannabinoid system. | endocannabinoid system evolution was estimated by searching for functional orthologs in the genomes of twelve phylogenetically diverse organisms: homo sapiens, mus musculus, takifugu rubripes, ciona intestinalis, caenorhabditis elegans, drosophila melanogaster, saccharomyces cerevisiae, arabidopsis thaliana, plasmodium falciparum, tetrahymena thermophila, archaeoglobus fulgidus, and mycobacterium tuberculosis. sequences similar to human endocannabinoid exon sequences were derived from filtered b ... | 2006 | 16434153 |
| identification and characterization of an interleukin-15 homologue from tetraodon nigroviridis. | interleukin-15 (il-15) plays an important role in adaptive immune systems in vertebrates with similar bioactivities to interleukin-2 (il-2). here we report molecular cloning, sequence analysis and distribution of an il-15 homologue from a pufferfish (tetraodon nigroviridis). it is located within a 3,088 bp genomic fragment, transcribed into a 1,056 bp mrna including 158 bp 5'utr (untranslated region), 519 bp orf (open reading frame) and 379 bp 3'utr. t. nigroviridis il-15 is constitutively detec ... | 2006 | 16455279 |
| many genes in fish have species-specific asymmetric rates of molecular evolution. | gene and genome duplication events increase the amount of genetic material that might then contribute to an increase in the genomic and phenotypic complexity of organisms during evolution. thus, it has been argued that there is a relationship between gene copy number and morphological complexity and/or species diversity. this hypothesis implies that duplicated genes have subdivided or evolved novel functions compared to their pre-duplication proto-orthologs. such a functional divergence might be ... | 2006 | 16466575 |
| proceedings of the smbe tri-national young investigators' workshop 2005. lineage-specific expansions and contractions of the bitter taste receptor gene repertoire in vertebrates. | the sense of bitter taste plays a critical role in how organisms avoid generally bitter toxic and harmful substances. previous studies revealed that there were 25 intact bitter taste receptor (t2r) genes in humans and 34 in mice. however, because the recent chicken genome project reported only three t2r genes, it appears that extensive gene expansions occurred in the lineage leading to mammals or extensive gene contractions occurred in the lineage leading to birds. here, i examined the t2r gene ... | 2006 | 16484289 |
| purification and characterization of recombinant pufferfish (takifugu rubripes) leptin. | synthetic cdna encoding pufferfish (takifugu rubripes) leptin (pflep) was prepared according to the published sequence. the pflep, transformed into escherichia coli and expressed upon induction with nalidixic acid, was found almost entirely in the insoluble inclusion bodies (ibs). the proteins were solubilized, refolded and purified to homogeneity by anion-exchange chromatography and gel-filtration. the respective yield of dimers and monomers was 50-100mg from 5l of fermentation culture. circula ... | 2008 | 18191858 |
| uneven evolutionary rates of bradykinin b1 and b2 receptors in vertebrate lineages. | bradykinin acts through two receptor subtypes in mammals and generates a variety of responses including pain, inflammation and hypotension. the evolutionary history of the bradykinin system has been unclear due to shortage of information outside mammals. we describe here two receptor subtypes and the bradykinin precursor in three species of bony fish (the zebrafish danio rerio, the japanese pufferfish takifugu rubripes, and the green spotted pufferfish tetraodon nigroviridis) and chicken and ana ... | 2006 | 16530355 |
| characterization of cd8+ leukocytes in fugu (takifugu rubripes) with antiserum against fugu cd8alpha. | we have investigated the characteristics of cd8+ leukocytes by using an anti-cd8alpha antiserum raised in mouse by dna-immunization. the magnetically sorted cd8alpha+ peripheral blood leukocyte (pbl) population comprised lymphocytes/thrombocytes and monocytes, whereas cd8alpha- pbls consisted of lymphocytes/thrombocytes, monocytes, and neutrophils. expression analysis demonstrated that both groups of cells expressed the cd3epsilon and tcralpha genes. the cd8alpha and cd8beta genes were detected ... | 2008 | 18262266 |
| haptoglobin, a hemoglobin-binding plasma protein, is present in bony fish and mammals but not in frog and chicken. | hemoglobin (hb) released from erythrocytes may cause oxidation of lipids and proteins. haptoglobin (hp), which occurs in the plasma of all mammals, binds free hb and inhibits its oxidative activity. it is not known whether this protective protein also exists in lower vertebrates. by analyzing available genomic sequences, we have found that bony fish, but not more primitive animals, have a gene coding for a protein homologous to mammalian hp. furthermore, we show that this protein is present in t ... | 2006 | 16537503 |
| evolution of cis elements in the differential expression of two hoxa2 coparalogous genes in pufferfish (takifugu rubripes). | sequence divergence in cis-regulatory elements is an important mechanism contributing to functional diversity of genes during evolution. gene duplication and divergence provide an opportunity for selectively preserving initial functions and evolving new activities. many vertebrates have 39 hox genes organized into four clusters (hoxa-hoxd); however, some ray-finned fishes have extra hox clusters. there is a single hoxa2 gene in most vertebrates, whereas fugu (takifugu rubripes) and medaka (oryzi ... | 2006 | 16569696 |
| phylogeny and evolution of class-i helical cytokines. | the class-i helical cytokines constitute a large group of signalling molecules that play key roles in a plethora of physiological processes including host defence, immune regulation, somatic growth, reproduction, food intake and energy metabolism, regulation of neural growth and many more. despite little primary amino acid sequence similarity, the view that all contemporary class-i helical cytokines have expanded from a single ancestor is widely accepted, as all class-i helical cytokines share a ... | 2006 | 16614377 |
| 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 thi ... | 2004 | 15246529 |
| monoclonal antibodies recognising serum immunoglobulins and surface immunoglobulin-positive cells of puffer fish, torafugu (takifugu rubripes). | immunoglobulin of the torafugu, takifugu rubripes, was purified by a combination of precipitation by low ionic strength dialysis and gel filtration. the ig was used to immunise mice for the production of monoclonal antibody (mab). supernatants of hybridoma cultures were screened by enzyme-linked immunosorbent assay using purified-torafugu ig-coated plates, and two stable hybridomas producing mabs against torafugu ig were obtained. sodium dodecyl sulphate-polyacrylamide gel electrophoresis under ... | 2004 | 15276601 |
| human homologs of the putative g protein-coupled membrane progestin receptors (mpralpha, beta, and gamma) localize to the endoplasmic reticulum and are not activated by progesterone. | the steroid hormone progesterone exerts pleiotrophic functions in many cell types. although progesterone controls transcriptional activation through binding to its nuclear receptors, it also initiates rapid nongenomic signaling events. recently, three putative membrane progestin receptors (mpralpha, beta, and gamma) with structural similarity to g protein-coupled receptors have been identified. these mpr isoforms are expressed in a tissue-specific manner and belong to the larger, highly conserve ... | 2006 | 16959873 |
| involvement of host recognition by oncomiracidia and post-larval survivability in the host specificity of heterobothrium okamotoi (monogenea: diclidophoridae). | heterobothrium okamotoi, a monogenean gill parasite, shows high host specificity for tiger puffer, takifugu rubripes. in the present study, in vivo and in vitro experimental infections were conducted using various fish species, including t. rubripes, to understand the mechanisms of specificity. in in vivo experiments, t. rubripes, grass puffer, takifugu niphobles, olive flounder, paralichthys olivaceus, and red sea bream, pagrus major, were exposed to oncomiracidia of h. okamotoi labelled with a ... | 2007 | 17055510 |
| genomics and mapping of teleostei (bony fish). | until recently, the human genome project held centre stage in the press releases concerning sequencing programmes. however, in october 2001, it was announced that the japanese puffer fish (takifugu rubripes, fugu) was the second vertebrate organism to be sequenced to draft quality. briefly, the spotlight was on fish genomes. there are currently two other fish species undergoing intensive sequencing, the green spotted puffer fish (tetraodon nigroviridis) and the zebrafish (danio rerio). but this ... | 2003 | 18629122 |
| teleost tlr22 recognizes rna duplex to induce ifn and protect cells from birnaviruses. | tlr22 occurs exclusively in aquatic animals and its role is unknown. herein we show that the fugu (takifugu rubripes) (fg)tlr3 and fgtlr22 link the ifn-inducing pathway via the fg toll-il-1r homology domain-containing adaptor protein 1(fgticam-1, or trif) adaptor in fish cells. fgtlr3 resides in endoplasmic reticulum and recognizes relatively short-sized dsrna, whereas fgtlr22 recognizes long-sized dsrna on the cell surface. on poly(i:c)-stimulated fish cells, both recruit fgticam-1, which in tu ... | 2008 | 18714020 |
| functional genome analysis indicates loss of 17beta-hydroxysteroid dehydrogenase type 2 enzyme in the zebrafish. | among the family of 17beta-hydroxysteroid dehydrogenases, the type 2 (17beta-hsd 2) is the main enzyme responsible for inactivation of estrogens and androgens, catalyzing the oxidation of the c17 hydroxyl group. 17beta-hsd 2 has been studied only in mammals, its occurrence and function in other vertebrates hardly known. we investigated the presence of homologs in non-mammalian species and found sequences of 17beta-hsd 2 and its closest homolog 11beta-hsd 2 in zebrafish (danio rerio), takifugu ru ... | 2007 | 17085046 |
| profiling of maternal and developmental-stage specific mrna transcripts in atlantic halibut hippoglossus hippoglossus. | cdna libraries were constructed from the following developmental stages (tissues) of the atlantic halibut (hippoglossus hippoglossus): 2-cell stage (embryos), 1 day-old yolk sac larvae (trunk) and juvenile (fast skeletal muscle). a total of 4249 high quality expressed sequence tags from the three libraries were clustered into a partial transcriptome of 2124 putative genes. a large proportion of the gene clusters (48.3%) had no significant matches against known proteins. the most abundant ests of ... | 2007 | 17118579 |
| characterization of two duplicate zebrafish cb2-like cannabinoid receptors. | several cannabinoid receptors have been detected in many organisms. the best known are cb1, mainly expressed in the central nervous system and cb2 which is almost exclusively expressed in the periphery. here we report the molecular characterization of two duplicate cb2-like cannabinoid receptors from zebrafish (danio rerio) (zebrafish cb2a and zebrafish cb2b). the amino acid sequences of these receptors present 56% identity with takifugu rubripes cb2 sequence and 39% with human cb2 sequence and ... | 2007 | 17126498 |
| cdna sequencing and expression analysis of dicentrarchus labrax heme oxygenase-1. | the liver cdna encoding heme oxygenase--1 (ho-1) was sequenced from european sea bass (dicentrarchus labrax) (accession number no. ef139130). the ho-1 cdna was 1250 bp in nucleotide length and the open reading frame encoded 277 amino acid residues. the deduced amino acid sequence of the european sea bass had 75% and 50% identity with the amino acid sequences of tetraodontiformes (tetraodon nigroviridis and takifugu rubripes) and human ho-1 proteins, respectively. a short hydrophobic transmembran ... | 2008 | 19116084 |
| characterization of two paralogous muscleblind-like genes from the tiger pufferfish (takifugu rubripes). | muscleblind-like (mbnl) proteins are required for terminal muscle differentiation in mammals. in this study we have identified two mbnl paralogues from the tiger pufferfish, tmbnl2a and tmbnl3, which are the first examples of non-mammalian mbnl genes. tmbnl2a and tmbnl3 were found in regions of conserved synteny and had a high degree of global conservation with their mammalian homologues. phylogenetic analysis showed that the t. rubripes genome contains one mbnl3 gene and two copies of mbnl1 and ... | 2007 | 17157048 |
| pan-vertebrate toll-like receptors during evolution. | human toll-like receptors (tlrs) recognize pathogen-associated molecular patterns (pamps) to raise innate immune responses. the human tlr family was discovered because of its sequence similarity to fruit fly (drosophila) toll, which is involved in an anti-fungal response. in this review, we focus on the origin of the vertebrate tlr family highlighted through functional and phylogenetic analyses of tlrs in non-mammalian vertebrates. recent extensive genome projects revealed that teleosts contain ... | 2008 | 19506737 |
| immobilization antibodies of tiger puffer takifugu rubripes induced by i.p. injection against monogenean heterobothrium okamotoi oncomiracidia do not prevent the infection. | we examined whether infection by the monogenean heterobothrium okamotoi induces production of specific antibodies against oncomiracidia and their cilia, larvae on the gills, and adults on the branchial cavity wall of tiger puffer takifugu rubripes. we also investigated whether specific antibody production participates in acquired protection against h. okamotoi. sera from persistently infected fish immobilized h. okamotoi oncomiracidia 89 days after exposure and antibody levels (measured by enzym ... | 2007 | 17234044 |
| differential regulation of multiple alternatively spliced transcripts of myod. | splice variants of the basic helix-loop-helix myoblast determination factor (myod) have not been previously found in vertebrates. here we report the identification and characterization of three alternative transcripts of a myod paralogue from the tiger pufferfish (takifugu rubripes). the t. rubripes myod1 gene (tmyod1) has 3 exons and 2 introns and it is present on scaffold 104, in a region of conserved synteny with zebrafish. the isoform tmyod1-alpha is a putative protein of 281 residues that c ... | 2007 | 17292566 |
| short and long peptidoglycan recognition proteins (pgrps) in zebrafish, with findings of multiple pgrp homologs in teleost fish. | peptidoglycan recognition protein (pgrp) specifically binds to peptidoglycan and is considered to be one of the pattern recognition proteins in the innate immunity of insect and mammals. using a database mining approach and rt-pcr, multiple peptidoglycan recognition protein (pgrp) like genes have been discovered in fish including zebrafish danio rerio, japanese pufferfish takifugu rubripes and spotted green pufferfish tetraodon nigroviridis. they share the common features of those pgrps in arthr ... | 2007 | 17296228 |
| cloning of the cdna for murine von willebrand factor and identification of orthologous genes reveals the extent of conservation among diverse species. | interaction of von willebrand factor (vwf) with circulating platelets promotes hemostasis when a blood vessel is injured. the a1 domain of vwf is responsible for the initial interaction with platelets and is well conserved among species. knowledge of the cdna and genomic dna sequences for human vwf allowed us to predict the cdna sequence for murine vwf in silico and amplify its entire coding region by rt-pcr. the murine vwf cdna has an open reading frame of 8,442 bp, encoding a protein of 2,813 ... | 2007 | 17497430 |
| genomics, evolution, and expression of tbpl2, a member of the tbp family. | tbpl2 is the most recently discovered and less characterized member of the tata box binding protein (tbp) family that also comprises tbp, tata box binding protein-like 1 (tbpl1), and drosophila melanogaster tbp related factor (trf). in this paper we report our in silico and in vitro data on (i) the genomics of the tbpl2 gene in homo sapiens, pan troglodytes, mus musculus, rattus norvegicus, gallus gallus, xenopus tropicalis, and takifugu rubripes; (ii) its evolution and phylogenetic relationship ... | 2007 | 17570761 |
| foxk1 splice variants show developmental stage-specific plasticity of expression with temperature in the tiger pufferfish. | foxk1 is a member of the highly conserved forkhead/winged helix (fox) family of transcription factors and it is known to play a key role in mammalian muscle development and myogenic stem cell function. the tiger pufferfish (takifugu rubripes) orthologue of mammalian foxk1 (tfoxk1) has seven exons and is located in a region of conserved synteny between pufferfish and mouse. tfoxk1 is expressed as three alternative transcripts: tfoxk1-alpha, tfoxk1-gamma and tfoxk1-delta. tfoxk1-alpha is the ortho ... | 2007 | 17873000 |
| cg dinucleotide clustering is a species-specific property of the genome. | cytosines at cytosine-guanine (cg) dinucleotides are the near-exclusive target of dna methyltransferases in mammalian genomes. spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. the loci where cg dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as cpg islands. currently, cpg islands are solely defined by base compositional ... | 2007 | 17932072 |
| control of kidney, eye and limb expression of bmp7 by an enhancer element highly conserved between species. | bmp7 is expressed in numerous tissues throughout development and is required for morphogenesis of the eye, hindlimb and kidney. in this study we show that the majority if not all of the cis-regulatory sequence governing expression at these anatomical sites during development is present in approximately 20 kb surrounding exon 1. in eye, limb and kidney, multiple distinct enhancer elements drive bmp7 expression within each organ. in the eye, the elements driving expression in the pigmented epithel ... | 2007 | 17936743 |
| divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis. | myosin heavy chain genes (myhs) are the most important functional domains of myosins, which are highly conserved throughout evolution. the human genome contains 15 myhs, whereas the corresponding number in teleost appears to be much higher. although teleosts comprise more than one-half of all vertebrate species, our knowledge of myhs in teleosts is rather limited. a comprehensive analysis of the torafugu (takifugu rubripes) genome database enabled us to detect at least 28 myhs, almost twice as m ... | 2007 | 17940200 |
| the evolution of galactose alpha2,3-sialyltransferase: ciona intestinalis st3gal i/ii and takifugu rubripes st3gal ii sialylate galbeta1,3galnac structures on glycoproteins but not glycolipids. | sialyltransferases are a family of enzymes catalyzing the transfer of sialic acid residues to terminal non-reducing positions of oligosaccharide chains of glycoproteins and glycolipids. although expression of sialic acid is well documented in animals of the deuterostomian lineage, sialyltransferases have been predominantly described for relatively recent vertebrate lineages such as birds and mammals. this study outlines the characterization of the only sialyltransferase gene found in the tunicat ... | 2008 | 17973185 |
| putative prion protein from fugu (takifugu rubripes). | prion proteins (prp) of mammals, birds, reptiles and amphibians have been successfully cloned, expressed and purified in sufficient yields to enable 3d structure determination by nmr spectroscopy in solution. more recently, prp ortholog genes have also been identified in several fish species, based on sequence relationships with tetrapod prps. even though the sequence homology of fish prps to tetrapod prps is below 25%, structure prediction programs indicate a similar organization of the 3d stru ... | 2008 | 18070106 |
| retinoic acid regulation of the mesp-ripply feedback loop during vertebrate segmental patterning. | the mesp bhlh genes play a conserved role during segmental patterning of the mesoderm in the vertebrate embryo by specifying segmental boundaries and anteroposterior (a-p) segmental polarity. here we use a xenotransgenic approach to compare the transcriptional enhancers that drive expression of the mesp genes within segments of the presomitic mesoderm (psm) of different vertebrate species. we find that the genomic sequences upstream of the mespb gene in the pufferfish takifugu rubripes (tr-mespb ... | 2008 | 18261720 |
| inhibition of na currents by the toxin extracts from puffer fishes captured in the sea coast of japan. | the inhibitory effects of toxin extracted from muscle or liver of five different puffer fishes (hereafter referred as puffer(s)) captured on the japanese sea coast were examined on voltage-dependent sodium current (i(na)) recorded from dissociated single rat hippocampal ca1 neurons. the inhibitory effects estimated from ic(50) values of toxin extracts on i(na) were in the order of takifugu vermicularis > lagocephalus wheeleri > canthigaster rivulata > takifugu rubripes > arothron reticularis fro ... | 2010 | 20637221 |
| characterization and expression analysis of an interleukin-7 homologue in the japanese pufferfish, takifugu rubripes. | an interleukin-7 (il-7) gene has been cloned and sequenced within the japanese pufferfish, takifugu rubripes (fugu), providing the first conclusive evidence for the existence of il-7 in teleosts. the il-7 cdna was composed of 1438 bp, with a 117 bp 5'-utr, an 826 bp 3'-utr containing two mrna instability motifs, and a 498 bp orf which translates into a peptide of 166 amino acid residues. the fugu il-7 peptide contained a predicted signal peptide of 19 amino acid residues and the il-7/9 family si ... | 2008 | 18266867 |
| annotation of expressed sequence tags for the east african cichlid fish astatotilapia burtoni and evolutionary analyses of cichlid orfs. | the cichlid fishes in general, and the exceptionally diverse east african haplochromine cichlids in particular, are famous examples of adaptive radiation and explosive speciation. here we report the collection and annotation of more than 12,000 expressed sequence tags (ests) generated from three different cdna libraries obtained from the east african haplochromine cichlid species astatotilapia burtoni and metriaclima zebra. | 2008 | 18298844 |