| identification and functional analysis of an ovarian form of the egg activation factor phospholipase c zeta (plc?) in pufferfish. | recent studies suggest that egg activation in mammals is triggered by a sperm-specific phospholipase c, plczeta. in other vertebrate species such as medaka fish, chickens, and quail, plczeta is also expressed as a testis-specific mrna. functional studies suggest that plczeta plays a similar role as a trigger of egg activation in these species. here, we report the identification of plczeta orthologues in pufferfish species takifugu rubripes (fugu) and tetraodon nigroviridis (tetraodon). unexpecte ... | 2011 | 21268182 |
| the g protein-coupled receptors in the pufferfish takifugu rubripes. | guanine protein-coupled receptors (gpcrs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. they form the single, biggest drug-target family due to their versatility of action and their role in several physiological functions, being active players in detecting the presence of light, a variety of smells and tastes, amino acids, nucleotides, lipids, chemicals etc. in th ... | 2011 | 21342560 |
| 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 |
| phylogenetic and chromosomal analyses of multiple gene families syntenic with vertebrate hox clusters. | ever since the theory about two rounds of genome duplication (2r) in the vertebrate lineage was proposed, the hox gene clusters have served as the prime example of quadruplicate paralogy in mammalian genomes. in teleost fishes, the observation of additional hox clusters absent in other vertebrate lineages suggested a third tetraploidization (3r). because the hox clusters occupy a quite limited part of each chromosome, and are special in having position-dependent regulation within the multi-gene ... | 2008 | 18803835 |
| [cloning and analysis of lyb gene from lampetra japonica]. | in the present study, three y-box cdnas, named as lyb1, lyb2, and lyb3, were cloned from the liver and oral gland of japanese lamprey (lampetra japonica) using reverse transcript-pcr (rt-pcr) and rapid amplification of cdna ends (race) techniques. further bioinformatical analysis indicated that the three y-box genes of lamprey, i.e., lyb1, lyb2, and lyb3, encoded 331, 181, and 171 amino acids, respectively. the three amino acid sequences were homologically aligned with those from ciona intestina ... | 2008 | 19073576 |
| characterization of a hypoxia-response element in the epo locus of the pufferfish, takifugu rubripes. | animals respond to hypoxia by increasing synthesis of the glycoprotein hormone erythropoietin (epo) which in turn stimulates the production of red blood cells. the gene encoding epo has been recently cloned in teleost fishes such as the pufferfish takifugu rubripes (fugu) and zebrafish (danio rerio). it has been shown that the transcription levels of epo in teleost fishes increase in response to anemia or hypoxia in a manner similar to its human ortholog. however, the cis-regulatory element(s) m ... | 2010 | 21798198 |
| immobilization of cellulase from newly isolated strain bacillus subtilis td6 using calcium alginate as a support material. | bacillus subtilis td6 was isolated from takifugu rubripes, also known as puffer fish. cellulase from this strain was partially purified by ammonium sulphate precipitation up to 80% saturation, entrapped in calcium alginate beads, and finally characterized using cmc as the substrate. for optimization, various parameters were observed, including ph maximum, temperature maximum, sodium alginate, and calcium chloride concentration. ph maximum of the enzyme showed no changes before and after immobili ... | 2011 | 21947600 |
| 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 |
| 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 |
| conservation of a vitellogenin gene cluster in oviparous vertebrates and identification of its traces in the platypus genome. | vitellogenin (vtg) derivatives are the main egg-yolk proteins in most oviparous animal species, and are, therefore, key players in reproduction and embryo development. conserved synteny and phylogeny were used to identify a vtg gene cluster (vgc) that had been evolutionarily conserved in most oviparous vertebrates, encompassing the three linked vtgs on chicken (gallus gallus) chromosome 8. tandem arranged homologs to chicken vtgii and vtgiii were retrieved in similar locations in xenopus (xenopu ... | 2008 | 18343608 |
| cloning and expression analysis of recombination activating genes (rag1/2) in red snapper (lutjanus sanguineus). | recombination activating genes (rag1 and rag2), involved in the v(d)j recombination of immunoglobulin and t-cell receptor genes play a crucial role in the adaptive immune response in vertebrates. the expression of these genes was required for the proper development and maturity of lymphocytes so that they can be used as useful markers to evaluate the development of lymphoid organ. in this paper, the cdna of rag1 and rag2 in red snapper, lutjanus sanguineus were cloned by homological cloning and ... | 2012 | 22266137 |
| osmotic regulation of a novel flavin-containing monooxygenase in primary cultured cells from rainbow trout (oncorhynchus mykiss). | a cdna encoding a hepatic isoform of flavin-containing monooxygenase (hfmo) (ef063736) containing an open reading frame of 1792 base pairs (bp) and encoding 554 amino acids was cloned and sequenced from liver mrna of rainbow trout (oncorhynchus mykiss). the genomic sequence of hfmo was also characterized and was 4.379 kilobases, possessing 10 exons and 9 introns (eu519462). structural analysis of the promoter region showed several cis-acting elements including putative glucocorticoid and osmoreg ... | 2008 | 18372402 |
| novel fugu u6 promoter driven shrna expression vector for efficient vector based rnai in fish cell lines. | in fish species, although many studies on the use of rna interference (rnai) for gene function analysis have been reported, almost of them have utilized in vitro transcribed or synthesized small interfering rna (sirna), and there are a few studies which examined vector based rnai in fish species. in this study, we have identified u6 promoter of fugu (takifugu rubripes), and utilized it for expression of short hairpin rna (shrna) in fish cell lines. using northern blot analysis, we confirmed succ ... | 2008 | 18452704 |
| 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 |
| sequence and structural analysis of 4snc-tudor domain protein from takifugu rubripes. | the fugu sn4tdr protein belongs to an evolutionarily conserved family, consisting of four repeat staphylococcal nuclease-like domains (sn1-sn4) at the n-terminus followed by tudor and sn-like domains (tsn). sequence analysis showed that the c-terminal tsn domain is composed of a complete sn-like domain interdigitated with a tudor domain. in despite of low level of sequence identities, five sn-like domains have a few conserved amino acids that may play essential roles in the function of the prote ... | 2009 | 20198186 |
| histopathological studies on vibrio harveyi- infected tiger puffer, takifugu rubripes (temminck et schlegel), cultured in japan. | vibrio harveyi infection occurred with a moderate mortality in tiger puffer, takifugu rubripes (temminck et schlegel), in autumn 2007, at a mariculture farm in western japan. the diseased fish showed nodular lesions in the branchial chamber and the inner surface of the operculum. histopathologically, the lesions comprised granulation tissue containing many suppurative foci allowing propagation of the bacteria and granuloma encapsulating abscesses with a decrease in bacteria. the bacteria were di ... | 2010 | 20726939 |
| myogenin in model pufferfish species: comparative genomic analysis and thermal plasticity of expression during early development. | myogenin (myog) is a muscle-specific basic helix-loop-helix transcription factor that plays an essential role in the specification and differentiation of myoblasts. the myogenin genes from the tiger pufferfish, takifugu rubripes, and green-spotted pufferfish, tetraodon nigroviridis, were cloned and a comparative genomic analysis performed. the gene encoding myogenin is composed of three exons and has a relatively similar genomic structure in t. rubripes, t. nigroviridis and human. introns 1 and ... | 2006 | 20483233 |
| comparative proteomics analysis of midgut samples from takifugu rubripes exposed to excessive fluoride: initial molecular response to fluorosis. | comparative proteomic analysis was performed to identify proteins in the midgut of takifugu rubripes (fugu) in response to excessive fluoride. sixteen fish were randomly divided into a control group and an experimental group. the control group was raised in soft water alone (f?=?0.4 mg/l), whereas the experimental group was raised in the soft water with sodium fluoride at a high concentration of 35 mg/l. after 3 days, proteins were extracted from the fish midgut and then subjected to two-dimensi ... | 2011 | 21466417 |
| integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. | the compact genome of fugu (takifugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. however, the fragmented nature of the fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. to extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of fugu and anchored the scaffolds of the assembly to the 22 chromosomes of fugu. the map consists of 1,2 ... | 2011 | 21551351 |
| a comparative gene index for the white sturgeon acipenser transmontanus. | sturgeons are archaic fishes phylogenetically distinct from teleosts. they represent an important niche for aquaculture, particularly for the production of caviar and high quality fillets, while many natural populations in various world areas are today threatened by extinction. knowledge of the sturgeon genome is limited, as it is the case of many other species of interest for fishery, aquaculture and conservation. sequences from non-normalized libraries of skin and spleen of the american sturge ... | 2008 | 21798149 |
| Purification, characterization and cDNA cloning of a trypsin from the hepatopancreas of snakehead (Channa argus). | A trypsin was purified from the hepatopancreas of snakehead (Channa argus) by ammonium sulfate fractionation and a series of column chromatographies including DEAE-Sepharose, Sephacryl S-200 HR and Hi-Trap Capto-Q. The molecular mass of the purified trypsin was about 22kDa, as estimated by SDS-PAGE. The optimum pH and temperature of the purified trypsin were 9.0 and 40°C, respectively. The trypsin was stable in the pH range of 7.5-9.5 and below 45°C. The enzymatic activity was strongly inhibited ... | 2011 | 22155550 |
| structural, gene expression, and functional analysis of the fugu (takifugu rubripes) insulin-like growth factor binding protein-4 gene. | the insulin-like growth factor (igf) signaling pathway is a conserved pathway that regulates animal development, growth, metabolism, reproduction, and aging. the biological actions of igfs are modulated by igf-binding proteins (igfbps). although the structure and function of fish igfbp-1, -2, -3, and -5 have been elucidated, there is currently no report on the full-length structure of a fish igfbp-4 nor its biological action. in this study, we cloned and characterized the igfbp-4 gene from fugu. ... | 2009 | 19091910 |
| comparative proteomics analysis of cardiac muscle samples from pufferfish takifugu rubripes exposed to excessive fluoride: initial molecular response to fluorosis. | comparative proteomics was performed to identify proteins in the cardiac muscle of takifugu rubripes in initial response to excessive fluoride. sixteen fish were randomly divided into a control group and an experimental group. the control group was raised in softwater alone (f(-) = 0.4 mg/l), and the experimental group was raised in the same water with sodium fluoride at a high concentration of 35 mg/l. after 3 days, proteins were extracted from the fish cardiac muscle and then were subjected to ... | 2009 | 19778249 |
| plasma protein binding of tetrodotoxin in the marine puffer fish takifugu rubripes. | to elucidate the involvement of plasma protein binding in the disposition of tetrodotoxin (ttx) in puffer fish, we used equilibrium dialysis to measure protein binding of ttx in the plasma of the marine puffer fish takifugu rubripes and the non-toxic greenling hexagrammos otakii, and in solutions of bovine serum albumin (bsa) and bovine alpha-1-acid glycoprotein (agp). ttx (100-1000 microg/ml) bound to protein in t. rubripes plasma with low affinity in a non-saturable manner. the amount of bound ... | 2010 | 19778549 |
| short promoters in viral vectors drive selective expression in mammalian inhibitory neurons, but do not restrict activity to specific inhibitory cell-types. | short cell-type specific promoter sequences are important for targeted gene therapy and studies of brain circuitry. we report on the ability of short promoter sequences to drive fluorescent protein expression in specific types of mammalian cortical inhibitory neurons using adeno-associated virus (aav) and lentivirus (lv) vectors. we tested many gene regulatory sequences derived from fugu (takifugu rubripes), mouse, human, and synthetic composite regulatory elements. all fugu compact promoters ex ... | 2009 | 19949461 |
| characterisation of conserved non-coding sequences in vertebrate genomes using bioinformatics, statistics and functional studies. | we recently identified approximately 1400 conserved non-coding elements (cnes) shared by the genomes of fugu (takifugu rubripes) and human that appear to be associated with developmental regulation in vertebrates [woolfe, a., goodson, m., goode, d.k., snell, p., mcewen, g.k., vavouri, t., smith, s.f., north, p., callaway, h., kelly, k., walter, k., abnizova, i., gilks, w., edwards, y.j.k., cooke, j.e., elgar, g., 2005. highly conserved non-coding sequences are associated with vertebrate developm ... | 2006 | 20483234 |
| novel mannose-specific lectins found in torafugu, takifugu rubripes: a review. | in earlier work, we identified a novel mannose-specific lectin, termed pufflectin-s, from the skin mucus of torafugu, takifugu rubripes. we here make a brief review on the lectin. the amino acid sequence of pufflectin-s shares sequence homology with mannose-binding lectins of monocotyledonous plants, and has conserved two of three carbohydrate recognition domains, qdnvy motifs, of these plant lectins. by site-directed mutagenesis, we verified that the qdnvy motif in the n-terminal region was cri ... | 2006 | 20483241 |
| permanent genetic resources added to molecular ecology resources database 1 december 2012-31 january 2013. | this article documents the addition of 268 microsatellite marker loci to the molecular ecology resources database. loci were developed for the following species: alburnoides bipunctatus, chamaerops humilis, chlidonias hybrida, cyperus papyrus, fusarium graminearum, loxigilla barbadensis, macrobrachium rosenbergii, odontesthes bonariensis, pelteobagrus vachelli, posidonia oceanica, potamotrygon motoro, rhamdia quelen, sarotherodon melanotheron heudelotii, sibiraea angustata, takifugu rubripes, ta ... | 2013 | 23521844 |
| molecular cloning and expression of retinoic-acid synthesizing enzyme raldh2 from takifugu rubripes. | retinaldehyde dehydrogenases (raldhs) synthesize retinoic acid (ra), which is required for pattern formation and organogenesis during embryogenesis. to elucidate the common role of ra on vertebrate embryos, we first sought to clone a homologous gene to human raldh2 from fugu, takifugu rubripes. we cloned a 1837 bp cdna that encodes fugu raldh. the deduced amino acid sequence of the fugu raldh comprises 502 amino acids. the fugu raldh showed highest sequence identity to zebrafish, danio rerio, ra ... | 2006 | 20483243 |
| transcriptional regulatory regions of gap43 needed in developing and regenerating retinal ganglion cells. | mammals and fish differ in their ability to express axon growth-associated genes in response to cns injury, which contributes to the differences in their ability for cns regeneration. previously we demonstrated that for the axon growth-associated gene, gap43, regions of the rat promoter that are sufficient to promote reporter gene expression in the developing zebrafish nervous system are not sufficient to promote expression in regenerating retinal ganglion cells in zebrafish. recently, we identi ... | 2010 | 20034105 |
| toxicity of pufferfish takifugu rubripes cultured in netcages at sea or aquaria on land. | marine pufferfish (family tetraodontidae) are believed to accumulate tetrodotoxin (ttx) mainly in liver and ovary through the food chain by ingesting ttx-bearing organisms such as starfish, gastropods, crustacean, flatworms, ribbonworms, etc. consequently, it is hypothesized that non-toxic pufferfish can be produced if they are cultured with ttx-free diets in netcages at sea or aquaria on land, where the invasion of ttx-bearing organisms is completely shut off. to confirm this hypothesis, more t ... | 2006 | 20483246 |
| molecular cloning, functional characterization and phylogenetic analysis of trail in japanese pufferfish takifugu rubripes. | in this study, the complementary dna (cdna) of japanese pufferfish takifugu rubripes tumour necrosis factor-related apoptosis-inducing ligand (trail) was cloned by reverse-transcription pcr. the open reading frame of the trail consisted of 870 bases. the deduced amino-acid sequence of the trail showed a high homology with the sequences of other teleosts. recombinant soluble trail was fused with a small ubiquitin-related modifier gene to enhance the soluble expression level in escherichia coli bl ... | 2011 | 21884110 |
| Characterisation, expression and ontogeny of interleukin-6 and its receptors in zebrafish (Danio rerio). | Interleukin-6 (IL-6) is one of the most pleiotropic cytokines due to its importance in both innate and adaptive immune responses and other physiological processes. In this study, we identified the zebrafish (Danio rerio) IL-6 homologue by investigating the synteny between the human (Homo sapiens), the fugu (Takifugu rubripes) and the zebrafish genome. Although zebrafish IL-6 showed a low sequence homology with other IL-6 sequences in other species, it presented a high structural similarity to hu ... | 2011 | 22107841 |
| fox gene loci in takifugu rubripes and tetraodon nigroviridis genomes and comparison with those of medaka and zebrafish genomes. | members of the fox gene family of transcriptional regulators are essential for animal development and have been extensively studied in vertebrates. the mouse and human genomes contain at least 40 fox genes which are divided into 19 subclasses based on the sequence similarity of the highly conserved forkhead domain. using the genome sequence of the takifugu rubripes and tetraodon nigroviridis , we examined the genomic complement of fox genes in these organisms to gain insight into the evolutio ... | 2011 | 22073989 |
| isolation of seven il-17 family genes from the japanese pufferfish takifugu rubripes. | in humans, the il-17 family is composed of six members (a-f). the a, e and f forms have been extensively studied in numerous mammalian species. however, there are few reports regarding il-17 expression in teleost. in this study, il-17 family genes were isolated from the japanese pufferfish (fugu) and their structure and expression profile were analyzed. screening of the fugu genome database revealed the existence of five scaffolds containing il-17 family homologous genes. scaffold_1 contained th ... | 2010 | 20144719 |
| proteomics analysis of liver samples from puffer fish takifugu rubripes exposed to excessive fluoride: an insight into molecular response to fluorosis. | comparative proteomics was performed to identify proteins in the liver of takifugu rubripes in response to excessive fluoride exposure. sixteen fish were randomly divided into a control group and an experimental group. the control group was raised in soft water alone (f(-) = 0.4 mg/l), and the experimental group was raised in the same water with sodium fluoride at a high concentration of 35 mg/l. after 3 days, proteins were extracted from the fish livers and then subjected to two-dimensional pol ... | 2010 | 20146379 |
| an anti-apoptotic b-cell lymphoma-2 (bcl-2) from channa striatus: sequence analysis and delayed and advanced gene expression in response to fungal, bacterial and poly i:c induction. | b-cell lymphoma-2 (bcl-2) is a suppressor of apoptosis and inhibits the caspase dependent apoptosis pathway. in this study, we report molecular characterization of a cdna sequence encoded of bcl-2 from striped murrel, channa striatus. a partial cdna sequence of csbcl-2 was identified from the striped murrel cdna library during annotation. subsequently, the full length csbcl-2 cdna sequence was obtained by an internal sequencing method using a forward primer. the sequence contains 699 nucleotide ... | 2015 | 25128157 |
| a homolog of kunitz-type serine protease inhibitor from rock bream, oplegnathus fasciatus: molecular insights and transcriptional modulation in response to microbial and pamp stimulation, and tissue injury. | serine proteases and their inhibitors play vital roles in diverse biological processes. in this study, we identified and characterized cdna coding for a kunitz-type serine protease inhibitor (spi), which we designated as rbkspi, in a commercially important species, rock bream. the full-length cdna sequence of rbkspi consisted of 2452 bp with an open reading frame (orf) of 1521 bp encoding a polypeptide of 507 amino acid (aa) residues. in the rbkspi protein, manec, pkd, ldla, and two kunitz domai ... | 2015 | 26162478 |
| identification and characterization of pufflectin from the grass pufferfish takifugu niphobles and comparison of its expression with that of takifugu rubripes. | pufflectin found in takifugu rubripes (tr pufflectin) is the first animal lectin reported to show sequence similarity to monocotyledonous plant lectins. in the present study, we identified and characterized an orthologous lectin from takifugu niphobles (tn pufflectin), a species closely related to t. rubripes. tn pufflectin exhibits 86% identity to tr pufflectin with two conserved mannose-binding domains. tn pufflectin was mainly expressed in the skin, gills, brain, and muscles; however, it was ... | 2016 | 26777033 |
| in silico analysis of the conservation of human toxicity and endocrine disruption targets in aquatic species. | pharmaceuticals and industrial chemicals, both in the environment and in research settings, commonly interact with aquatic vertebrates. due to their short life-cycles and the traits that can be generalized to other organisms, fish and amphibians are attractive models for the evaluation of toxicity caused by endocrine disrupting chemicals (edcs) and adverse drug reactions. edcs, such as pharmaceuticals or plasticizers, alter the normal function of the endocrine system and pose a significant hazar ... | 2014 | 24392850 |
| β-defensin in nile tilapia (oreochromis niloticus): sequence, tissue expression, and anti-bacterial activity of synthetic peptides. | beta-defensins (β-defensins) are small cationic amphiphilic peptides that are widely distributed in plants, insects, and vertebrates, and are important for their antimicrobial properties. in this study, the β-defensin (onβ-defensin) gene of the nile tilapia (oreochromis niloticus) was cloned from spleen tissue. onβ-defensin has a genomic dna sequence of 674 bp and produces a cdna of 454 bp. sequence alignments showed that onβ-defensin contains three exons and two introns. sequence analysis of th ... | 2015 | 25871516 |
| cell-penetrating peptide delivery of biologically active oct4 protein into cultured takifugu rubripes spermary cells. | continuous cell culture of a puffer fish takifugu rubripes has been established for efficient delivery of exogenous genes or proteins to cultured fish cells. transcription factor oct4 was chosen for transduction into cultured fish cells because of its conserved structure and function between fish and mammals. in this work, the t. rubripes oct4 gene was cloned and expressed in escherichia coli as a recombinant protein by introducing cell-penetrating peptide (cpp) poly-arginine (11r) and 6his-tag ... | 2014 | 25199543 |
| serum glcnac-binding igm of fugu (takifugu rubripes) suppresses the growth of fish pathogenic bacteria: a novel function of teleost antibody. | n-acetyl-d-glucosamine (glcnac) is one of the components of peptidoglycan, a biopolymer in the bacterial cell wall. we purified a novel glcnac-binding protein, designated as fgbp-78, from sera of fugu (takifugu rubripes). the fgbp-78 is a heteromer of 78- and 25-kda subunits. moreover, fgbp-78 exerted remarkable inhibitory effects on the growth of both gram-positive and gram-negative bacteria, including ones virulent for marine fish species as well as non-pathogenic escherichia coli. these resul ... | 2013 | 23562572 |
| cloning, characterization and expression analysis of coagulation factor ii gene in grass carp (ctenopharyngodon idella). | here, we characterized the structure and function of the coagulation factor ii (fii) gene in grass carp and determined its role in coagulation mechanisms. the fii gene est was obtained using a constructed splenic transcriptome database; the full-length fii gene sequence was obtained by 3' and 5' race. the open reading frame (orf) of fii was cloned and the full-length gene was found to be 1718 bp, with an orf of 1572 bp; the gene contained a 25 bp 5'-untranslated region (utr) and 108 bp 3'-utr. t ... | 2015 | 26535692 |
| genomic regions of pufferfishes responsible for host specificity of a monogenean parasite, heterobothrium okamotoi. | the genetic mechanisms underlying host specificity of parasitic infections are largely unknown. after hatching, the larvae of the monogenean parasite, heterobothrium okamotoi, attach to the gill filaments of hosts and the post-larval worms develop there by consuming nutrients from the host. the susceptibility to h. okamotoi infection differs markedly among fish species. while this parasite can grow on tiger pufferfish (also called fugu), takifugu rubripes, it appears to be rejected by a close co ... | 2013 | 23872522 |
| inflammatory immune response by lipopolysaccharide-responsive nucleotide binding oligomerization domain (nod)-like receptors in the japanese pufferfish (takifugu rubripes). | some of nod-like receptors (nlrs), the cytosolic pattern recognition receptors form a multi-protein complex, inflammasome consisting of one or more nlrs, the adaptor protein asc and inflammatory caspase to generate mature inflammatory cytokines, interleukin (il)-1β and il-18. however, inflammasome-mediated inflammatory cascade involving any nlr member is unknown in a lower vertebrate like fish. also, inflammatory cytokine induction pathway in response to a specific ligand, namely bacterial lipop ... | 2016 | 26472618 |
| cytokine mediated immune responses in the japanese pufferfish (takifugu rubripes) administered with heat-killed lactobacillus paracasei spp. paracasei (06tca22) isolated from the mongolian dairy product. | the important role played by cytokines in host innate immunity and the interaction of subsets of immune and inflammatory cells through cytokines offer avenues for immune interventions. we investigated 16 cytokine gene responses in the japanese pufferfish, takifugu rubripes orally treated with a heat-killed lactic acid bacterium (lab), lactobacillus paracasei spp. paracasei (strain 06tca22) (lpp) isolated from a mongolian dairy product at 1mgg(-1)body weightd(-1) for 3days. additionally, we asses ... | 2013 | 23867289 |
| elevated cytokine responses to vibrio harveyi infection in the japanese pufferfish (takifugu rubripes) treated with lactobacillus paracasei spp. paracasei (06tca22) isolated from the mongolian dairy product. | with the aim of evaluating the effect of a mongolian dairy product derived lactobacillus paracasei spp. paracasei (strain 06tca22) (lpp) on the cytokine-mediated immune responses to vibrio harveyi infection, we examined 16 cytokine expressions in the japanese pufferfish, takifugu rubripes. fish were orally treated with the heat-killed lpp at 1 mg g(-1) body weight d(-1) for 3 days. at 24 h posttreatment, fish were infected by an intramuscular injection of 0.1 ml v. harveyi bacterial suspension ( ... | 2013 | 23769874 |
| cytokine responses in the japanese pufferfish (takifugu rubripes) head kidney cells induced with heat-killed probiotics isolated from the mongolian dairy products. | cytokine responses in the japanese pufferfish (takifugu rubripes) head kidney (hk) cells to heat-killed lactic acid bacteria probiotics isolated from the mongolian dairy products were investigated by transcriptomic examination. the hk cells were incubated with two heat-killed bacteria, namely lactobacillus paracasei spp. paracasei (strain 06tca22) and l. plantarum (strain 06cc2) and the responses of 16 cytokine genes at 0 (control), 1, 4, 8, 12, 24 and 48 h post-stimulation were assayed by multi ... | 2013 | 23422813 |
| the tnfα converting enzyme (tace) from ayu (plecoglossus altivelis) exhibits tnfα shedding activity. | tnfα converting enzyme (tace) is responsible for converting membrane-anchored tnfα to its soluble form in mammalian. however, the function and characteristics of tace in teleosts is unclear. in this study, we report the cloning of a cdna sequence of the patace from ayu, plecoglossus altivelis. patace encodes an 865-aa polypeptide, which is closest to the tace gene found in pufferfish (takifugu rubripes). patace mrna was detected in all the tissues tested, although it was considerably higher in l ... | 2015 | 25458310 |
| structure, tissue distribution and estrogen regulation of splice variants of the sea bream estrogen receptor α gene. | estrogen actions are mainly mediated by specific nuclear estrogen receptors (ers), for which different genes and a diversity of transcript variants have been identified, mainly in mammals. in this study, we investigated the presence of er splice variants in the teleost fish gilthead sea bream (sparus auratus), by comparison with the genomic organization of the related species takifugu rubripes. two exon2-deleted erα transcript variants were isolated from liver cdna of estradiol-treated fish. the ... | 2012 | 22579469 |
| molecular characterization of a cdna from the gilthead sea bream (sparus aurata) encoding a fish prion protein. | we have identified and characterized a cdna from the brain tissue of the highly commercial marine fish species, the gilthead sea bream (sparus aurata), which encodes a 496 amino acid residue protein sharing the organizational and structural features of the mammalian prion proteins. tissue mrna expression analyses revealed the presence of this transcript in various tissues of the gilthead sea bream including the brain, the spleen, and the heart. sequence comparison and phylogenetic analysis showe ... | 2007 | 17468028 |
| identification, characterization and expression of a novel cytokine m17 homologue (msh) in fish. | members of the interleukin 6 (il6)-cytokine subfamily of proteins are involved in numerous physiological processes including cellular development, inflammatory function, and acute phase and immune responses. previously, a cytokine-like gene named m17, which is closely associated with the il6 subfamily, has been identified in fish with no apparent orthologue in higher vertebrates. here, we cloned a novel cdna from japanese flounder, paralichthys olivaceus, which had significant identity but exhib ... | 2007 | 17950621 |
| positive feedback of hepatic angiotensinogen expression in silver sea bream (sparus sarba). | the renin-angiotensin system (ras) is involved in the maintenance of fluid homeostasis in vertebrates. production of the precursor protein, angiotensinogen, is regulated by other components within the ras. angiotensin ii (ang ii) stimulates the production and secretion of angiotensinogen in many mammalian models. however, the existence of a similar positive feedback mechanism for angiotensinogen has not been demonstrated for any non-mammalian species. in the present study, we have cloned the ang ... | 2007 | 17027145 |
| experimental infection of several fish species with the causative agent of kuchijirosho (snout ulcer disease) derived from the tiger puffer takifugu rubripes. | kuchijirosho (snout ulcer disease) is a fatal epidemic disease which affects the tiger puffer, takifugu rubripes, a commercial fish species in japan and korea. to assess the possibility that non-tiger puffer fish can serve as reservoirs of infection, 5 fish species were challenged by infection with the extracts of kuchijirosho-affected brains from cultured tiger puffer: grass puffer t. niphobles, fine-patterned puffer t. poecilonotus, panther puffer t. pardalis, red sea bream pagrus major, and b ... | 2001 | 11804418 |
| characterization of genes encoding prolactin and prolactin receptors in starry flounder platichthys stellatus and their expression upon acclimation to freshwater. | this study aims to investigate the genes encoding prolactin (prl) and prolactin receptors (prlr) and their tissue-specific expression in starry flounder platichthys stellatus. starry flounder prl gene consisting of five exons encodes an orf of 212 amino acid residue comprised of a putative signal peptide of 24 amino acids and a mature protein of 188 amino acids. it showed amino acid identities of 73 % with tuna thunnus thynnus, 71 % with black porgy acanthopagrus schlegelii, 69 % with nile tilap ... | 2013 | 22843312 |
| a single amino acid substitution can shift the optimum ph of dnase i for enzyme activity: biochemical and molecular analysis of the piscine dnase i family. | we purified four piscine deoxyribonucleases i (dnases i) from anguilla japonica, pagrus major, cryprus carpio and oreochromis mossambica. the purified enzymes had an optimum ph for activity of approximately 8.0, significantly higher than those of mammalian enzymes. cdnas encoding the first three of these piscine dnases i were cloned, and the sequence of the takifugu rubripes enzyme was obtained from a database search. nucleotide sequence analyses revealed relatively greater structural variations ... | 2004 | 15182937 |
| adaptation of pineal expressed teleost exo-rod opsin to non-image forming photoreception through enhanced meta ii decay. | photoreception by vertebrates enables both image-forming vision and non-image-forming responses such as circadian photoentrainment. over the recent years, distinct non-rod non-cone photopigments have been found to support circadian photoreception in diverse species. by allowing specialization to this sensory task a selective advantage is implied, but the nature of that specialization remains elusive. we have used the presence of distinct rod opsin genes specialized to either image-forming (retin ... | 2011 | 21416149 |
| characterization of muscle-regulatory gene, myod, from flounder (paralichthys olivaceus) and analysis of its expression patterns during embryogenesis. | specification and differentiation of skeletal muscle cells are driven by the activity of genes encoding members of the myogenic regulatory factors (mrfs). in vertebrates, the mrf family includes myod, myf5, myogenin, and mrf4. the mrfs are capable of converting a variety of nonmuscle cells into myoblasts and myotubes. to better understand their roles in fish muscle development, we isolated the myod gene from flounder (paralichthys olivaceus) and analyzed its structure and patterns of expression. ... | 2006 | 16362809 |
| expression and genomic organization of zonadhesin-like genes in three species of fish give insight into the evolutionary history of a mosaic protein. | the mosaic sperm protein zonadhesin (zan) has been characterized in mammals and is implicated in species-specific egg-sperm binding interactions. the genomic structure and testes-specific expression of zonadhesin is known for many mammalian species. all zonadhesin genes characterized to date consist of meprin a5 antigen receptor tyrosine phosphatase mu (mam) domains, mucin tandem repeats, and von willebrand (vwd) adhesion domains. here we investigate the genomic structure and expression of zonad ... | 2005 | 16303057 |
| genome size evolution in pufferfish: an insight from bac clone-based diodon holocanthus genome sequencing. | variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. | 2010 | 20569428 |
| description of embryonic development of spotted green pufferfish (tetraodon nigroviridis). | pufferfish species of the tetraodontidae family carry the smallest genomes among vertebrates. their compressed genomes are thought to be enriched for functional dna compared to larger vertebrate genomes, and they are important models for comparative genomics. the significance of pufferfish as model organisms in comparative genomics is due to the availability of two sequenced genomes, that of spotted green pufferfish (tetraodon nigroviridis) and fugu (takifugu rubripes). however, there is only a ... | 2014 | 25243591 |
| sequencing and characterization of the anadromous steelhead (oncorhynchus mykiss) transcriptome. | identifying the traits that differ between hatchery and wild fish may allow for pragmatic changes to hatchery practice. to meet those ends, we sequenced, assembled, and characterized the anadromous steelhead (oncorhynchus mykiss) transcriptome. using the illumina sequencing platform, we sequenced nearly 41million 76-mer reads representing 3.1 gbp of steelhead transcriptome. upon final assembly, this sequence data yielded 86,402 transcript scaffolds, of which, 66,530 (77%) displayed homology to p ... | 2014 | 24440488 |
| evolution of the myosin heavy chain gene myh14 and its intronic microrna mir-499: muscle-specific mir-499 expression persists in the absence of the ancestral host gene. | a novel sarcomeric myosin heavy chain gene, myh14, was identified following the completion of the human genome project. myh14 contains an intronic microrna, mir-499, which is expressed in a slow/cardiac muscle specific manner along with its host gene; it plays a key role in muscle fiber-type specification in mammals. interestingly, teleost fish genomes contain multiple myh14 and mir-499 paralogs. however, the evolutionary history of myh14 and mir-499 has not been studied in detail. in the presen ... | 2013 | 24059862 |
| identification of olfactory receptor genes in atlantic salmon salmo salar. | it has been hypothesized that salmonids use olfactory cues to return to their natal rivers and streams. the key components of the molecular pathways involved in imprinting and homing, however, are still unknown. aquatic chemical cues are received through the nares and into the nasal cavity that contains a single olfactory organ, the olfactory rosette. the olfactory rosette contains sensory neurons, each of which is thought to express only one olfactory receptor. if odorants are involved in salmo ... | 2012 | 22803724 |
| salmondb: a bioinformatics resource for salmo salar and oncorhynchus mykiss. | salmondb is a new multiorganism database containing est sequences from salmo salar, oncorhynchus mykiss and the whole genome sequence of danio rerio, gasterosteus aculeatus, tetraodon nigroviridis, oryzias latipes and takifugu rubripes, built with core components from gmod project, goparc system and the biomart project. the information provided by this resource includes gene ontology terms, metabolic pathways, snp prediction, cds prediction, orthologs prediction, several precalculated blast sear ... | 2011 | 22120661 |
| comparative genomics of duplicate γ-glutamyl transferase genes in teleosts: medaka (oryzias latipes), stickleback (gasterosteus aculeatus), green spotted pufferfish (tetraodon nigroviridis), fugu (takifugu rubripes), and zebrafish (danio rerio). | the availability of multiple teleost (bony fish) genomes is providing unprecedented opportunities to understand the diversity and function of gene duplication events using comparative genomics. here we examine multiple paralogous genes of γ-glutamyl transferase (ggt) in several distantly related teleost species including medaka, stickleback, green spotted pufferfish, fugu, and zebrafish. through mining genome databases, we have identified multiple ggt orthologs. duplicate (paralogous) ggt sequen ... | 2012 | 21898790 |
| comparative analysis of intronless genes in teleost fish genomes: insights into their evolution and molecular function. | this study assessed the relationship between the occurrence and function of intronless or single exon genes (seg) in the genome of five teleost species and their phylogenetic distance. the results revealed that takifugu rubripes, tetraodon nigroviridis, oryzias latipes, gasterosteus aculeatus and danio rerio genomes are respectively comprised of 2.83%, 3.42%, 4.49%, 4.35% and 4.02% segs. these segs encode for a variety of family proteins including claudins, olfactory receptors and histones that ... | 2011 | 21620332 |
| different phylogenomic approaches to resolve the evolutionary relationships among model fish species. | comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. to implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model sp ... | 2010 | 20591844 |
| alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons. | alternative splicing (as) is a mechanism by which the coding diversity of the genome can be greatly increased. rates of as are known to vary according to the complexity of eukaryotic species potentially explaining the tremendous phenotypic diversity among species with similar numbers of coding genes. little is known, however, about the nature or rate of as in teleost fish. here, we report the characteristics of as in teleost fish and classification and frequency of five canonical as types. we co ... | 2010 | 20383527 |
| characterization of c-c chemokine receptor subfamily in teleost fish. | chemokines and their receptors play important roles in nervous and immune systems. little information, however, exists concerning this gene family in teleost fish. in the present study, 17 c-c chemokine receptors genes were identified from danio rerio, 9 from gasterosteus aculeatus, 10 from oryzias latipes, 8 from takifugu rubripes and 5 from tetraodon nigroviridis. phylogenetic analysis showed that the orthologs to mammalian ccr6, 7, 8, 9 and ccrl1 receptors were evident in zebrafish, but the c ... | 2009 | 19022503 |
| gonadotropin hormone and receptor sequences from model teleost species. | fish offer some advantages for the study of vertebrate reproductive physiology. only a few of the genes encoding the components of the hypothalamic-pituitary-gonadal axis have been identified from model teleosts. this study describes a combination of database searching and molecular approaches to identify the fsh and lh gonadotropin beta-subunits (fshb and lhb, respectively), and the lh receptor (lhr) from two model teleost species: zebrafish (danio rerio) and fugu (takifugu rubripes). sequence ... | 2004 | 18248232 |
| evidence for positive selection in the tlr9 gene of teleosts. | toll-like receptors (tlrs) have been identified as key sensors of invading microbes by identifying pathogen-associated molecular patterns and activating innate immune responses. whereas purifying selection has been suggested in mammalian tlr9, evolutionary features of tlr9 in teleosts have not been investigated in detail. we therefore analysed tlr9 dna sequences of eight teleost species, including zebrafish (danio rerio), japanese flounder (paralichthys olivaceus), pufferfish (takifugu rubripes) ... | 2008 | 18164212 |
| global identification and comparative analysis of socs genes in fish: insights into the molecular evolution of socs family. | the suppressors of cytokine signaling (socs) family play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development of organisms. however, the family members in early vertebrate species and their evolutionary history and relationships remain largely unknown. in present study, totally 120 socs genes from various species were globally investigated, among of which 66 new socs genes were identified, including 55 socs genes from five ... | 2008 | 18029016 |
| evolution of the neuropeptide y family: new genes by chromosome duplications in early vertebrates and in teleost fishes. | despite sequence information from many vertebrates the evolution of the neuropeptide y (npy) family of peptides has been difficult to resolve, particularly among ray-finned fishes. we have used chromosomal location and sequence analyses to identify orthologs and gene duplicates in teleost fish genomes. our analyses support origin of npy and peptide yy (pyy) from a common ancestor in early vertebrate evolution through a chromosome duplication. we report here that the teleost tetraploidization gen ... | 2008 | 17950734 |
| a novel olfactory receptor gene family in teleost fish. | while for two of three mammalian olfactory receptor families (or and v2r) ortholog teleost families have been identified, the third family (v1r) has been thought to be represented by a single, closely linked gene pair. we identified four further v1r-like genes in every teleost species analyzed (danio rerio, gasterosteus aculeatus, oryzias latipes, tetraodon nigroviridis, takifugu rubripes). in the phylogenetic analysis these ora genes (olfactory receptor class a-related) form a single clade, whi ... | 2007 | 17717047 |
| a practical approach to phylogenomics: the phylogeny of ray-finned fish (actinopterygii) as a case study. | molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in dna technology. the inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new ph ... | 2007 | 17374158 |
| discovery of multiple beta-defensin like homologues in teleost fish. | using a database mining approach, multiple defensin like genes have been discovered for the first time in fish, in species including zebrafish danio rerio and the pufferfish, takifugu rubripes and tetraodon nigroviridis. they share the common features of vertebrate defensins, including small size, net cationic charge, and six conserved cysteines in the mature region. based on their cysteine arrangement, the identified fish defensin like peptides resemble beta-defensin family members in birds and ... | 2007 | 16540171 |
| [comparative structural analysis of myosin light chains and gene duplication in fish]. | origin and structure of myosin light chain (mlc) proteins have been studied by comparative analysis of fish mlc1, mlc2, and mlc3 genes encoding mlc1, mlc2, and mlc3, respectively. the exon-intron structure of these genes has been analyzed in zebrafish danio rerio, loach misgurnus fossilis, fugu takifugu rubripes, and nile puffer tetraodon fahaka. we propose that mlc1 and mlc3 are homologues genes originated by fish-specific whole genome duplication (paralogs). this is supported by high sequence ... | 2016 | 16521537 |
| structural comparison of promoter and coding sequence of type i collagen alpha 1 chain gene duplicates between zebrafish and flounder/fugu lineages. | alpha 1 chain (colalpha1(i)) and alpha 2 chain (colalpha2(i)) are universal components of type i collagen in tetrapods, but rainbow trout (oncorhynchus mykiss) and zebrafish (danio rerio) have a third: alpha 3 chain (colalpha3(i)). this study tests whether colalpha3(i) is a duplicate of colalpha1(i) by whole-genome duplication (wgd) that occurred early in the ray-fin fish lineage. we also examine how their promoter sequence was modified after wgd. we cloned colalpha1(i), colalpha2(i) and colalph ... | 2006 | 20483231 |
| multiple occurrences of spiggin genes in sticklebacks. | the threespine stickleback (gasterosteus aculeatus) is known to have a unique reproductive mode including male nest-building with a secreted glue-like protein named spiggin. spiggin is a key character for studying the molecular mechanism in the evolution of this intriguing nest-building behavior, since the glue-like protein is essential for nest-building. however, it is unclear whether spiggin is encoded by a single gene or multiple genes; there are conflicting reports on this point. to resolve ... | 2006 | 16500044 |
| fugu genome does not contain mitochondrial pseudogenes. | contrary to previous observations that fish genomes are devoid of nuclear mitochondrial pseudogenes, a genome-wide survey identified a large number of "recent" and "ancient" nuclear mitochondrial dna fragments (numts) in the whole-genome sequences of the fugu (takifugu rubripes), tetraodon nigroviridis, and zebrafish (danio rerio). we have analyzed the latest assembly (v4.0) of the fugu genome and show that, like the anopheles genome, the fugu nuclear genome does not contain mitochondrial pseudo ... | 2006 | 16386876 |
| new approach for fish breeding by chemical mutagenesis: establishment of tilling method in fugu (takifugu rubripes) with enu mutagenesis. | in fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. tilling (targeting induced local lesions in genomes) is a reverse genetics strategy that combines random chemical mutagenesis with high ... | 2013 | 24225309 |
| regulation of gene expression mediating indeterminate muscle growth in teleosts. | teleosts are unique among vertebrates due to their indeterminate muscle growth, i.e., continued production of neonatal muscle fibers until death. however, the molecular mechanism(s) underlying this property is unknown. here, we focused on the torafugu (takifugu rubripes) myosin heavy chain gene, myhm2528-1, which is specifically expressed in neonatal muscle fibers produced by indeterminate muscle growth. we examined the flanking region of myhm2528-1 through an in vivo reporter assay using zebraf ... | 2015 | 25842264 |
| the irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b. | genes of the iroquois ( iro/irx) family are highly conserved from drosophila to mammals and they have been implicated in a number of developmental processes. in flies, the iro genes participate in patterning events in the early larva and in imaginal disk specification. in vertebrates, the irx genes regulate developmental events during gastrulation, nervous system regionalization, activation of proneural genes and organ patterning. the iro genes in drosophila and the irx genes of mammals show a c ... | 2004 | 15064948 |
| genomic characterization and expression analysis of the first nonmammalian renin genes from zebrafish and pufferfish. | renin is a key enzyme in the renin-angiotensin system (ras), a pathway which plays an important physiological role in blood pressure and electrolyte homeostasis. the origin of the ras is believed to have accompanied early evolution of vertebrates. however, renin genes have so far only been unequivocally identified in mammals. whether or not a bona fide renin gene exists in nonmammalian vertebrates has been an intriguing question of physiological and evolutionary interest. using a genomic analyti ... | 2004 | 14645735 |
| identification of a novel adrenomedullin gene family in teleost fish. | adrenomedullin (am) is a multifunctional peptide known to form a hormone family with calcitonin gene-related peptide (cgrp) and amylin. we have cloned five distinct am cdnas from the pufferfish, takifugu rubripes, and named them tram-1, -2, -3, -4, and -5. judging from the deduced precursor sequences and processing pattern of the c-terminal mature peptides, trams may be divided into at least two groups; am-2 and -3, and am-1, -4, and possibly -5. phylogenetic analysis of the mature peptides, exo ... | 2003 | 14623291 |
| an active non-ltr retrotransposon with tandem structure in the compact genome of the pufferfish tetraodon nigroviridis. | the fish retrotransposable element zebulon encodes a reverse transcriptase and a carboxy-terminal restriction enzyme-like endonuclease, and is related phylogenetically to site-specific non-ltr retrotransposons from nematodes. zebulon was detected in the pufferfishes tetraodon nigroviridis and takifugu rubripes, as well as in the zebrafish danio rerio. structural analysis suggested that zebulon, in contrast to most non-ltr retrotransposons, might be able to retrotranspose as a partial tandem arra ... | 2003 | 12805276 |
| grouper (epinephelus coioides) tcr signaling pathway was involved in response against cryptocaryon irritans infection. | t cell activation is a complicated process accompanying with the activation of t cell receptor (tcr) signaling pathway, which is not well described in teleost fish. the initiation of this pathway depends on the interaction of membrane tcr co-receptors (e.g. cd4/8, cd3 and cd45) and a series of cytoplasmic protein tyrosine kinases (e.g. lck, fyn and zap70). cyptocaryon irritans is a ciliate pathogen of marine fish white spot disease causing huge economic lost in marine aquaculture. this parasite ... | 2017 | 28286257 |
| grouper (epinephelus coioides) bcr signaling pathway was involved in response against cryptocaryon irritans infection. | b cell antigen receptor (bcr) plays a crucial role in b cell development and antibody production. it comprises membrane immunoglobulin non-covalently associated with cd79a/cd79b heterodimer. after b cell activation, initial extracellular signals are transduced by bcr complex and amplified by two protein tyrosine kinases, lyn and syk, which then trigger various pathways. in the present study, we cloned grouper genes for bcr accessory molecules, eccd79a (669 bp) and eccd79b (639 bp), as well as tw ... | 2016 | 27514788 |
| analysis of the exon-intron structures of fish, amphibian, bird and mammalian hatching enzyme genes, with special reference to the intron loss evolution of hatching enzyme genes in teleostei. | using gene cloning and in silico cloning, we analyzed the structures of hatching enzyme gene orthologs of vertebrates. comparison led to a hypothesis that hatching enzyme genes of japanese eel conserve an ancestral structure of the genes of fishes, amphibians, birds and mammals. however, the exon-intron structure of the genes was different from species to species in teleostei: japanese eel hatching enzyme genes were 9-exon-8-intron genes, and zebrafish genes were 5-exon-4-intron genes. in the pr ... | 2007 | 17222522 |
| evolution of hox clusters in salmonidae: a comparative analysis between atlantic salmon (salmo salar) and rainbow trout (oncorhynchus mykiss). | we studied the genomic organization of hox genes in atlantic salmon (salmo salar) and made comparisons to that in rainbow trout (oncorhynchus mykiss), another member of the family salmonidae. we used these two species to test the hypothesis that the hox genes would provide evidence for a fourth round of duplication (4r) of this gene family given the recent polyploid ancestry of the salmonid fish. thirteen putative hox clusters were identified and 10 of these complexes were localized to the curre ... | 2005 | 16205980 |
| duplicated cytoglobin genes in teleost fishes. | cytoglobin is a recently discovered myoglobin-related o2-binding protein of vertebrates with uncertain function. it occurs as single-copy gene in mammals. here, we demonstrate the presence of two paralogous cytoglobin genes (cygb-1 and cygb-2) in the teleost fishes danio rerio, oryzias latipes, tetraodon nigroviridis, and takifugu rubripes. the globin-typical introns at positions b12.2 and g7.0 are conserved in both genes, whereas the c-terminal exon found in mammalian cytoglobin is absent in th ... | 2005 | 16199220 |
| iron bioavailability in larvae yellow snapper (lutjanus argentiventris): cloning and expression analysis of ferritin-h. | ferritin is a major intracellular iron storage protein in higher vertebrates and plays an important role in iron metabolism. in this study, ferritin h subunit was cloned from the larvae of yellow snapper, lutjanus argentiventris, by rapid amplification of cdna ends (race) following in silico transcriptome analysis. the full-length cdnas of the lafeh was 1231 bp in length encoding 177 amino acids with a predicted molecular mass (mw) about 20.82 kda and theoretical isoelectric point (pi) of 5.79. ... | 2014 | 24561126 |
| xena, a full-length basal retroelement from tetraodontid fish. | mobile genetic elements are ubiquitous throughout the eukaryote superkingdom. we have sequenced a highly unusual full-length retroelement from the fugu fish, takifugu rubripes. this element, which we have named xena, is similar in structure and sequence to the penelope retroelement from drosophila virilis and consists of a single long open reading frame containing a reverse transcriptase domain flanked by identical direct long terminal repeat (ltr) sequences. these ltrs show an organization simi ... | 2002 | 11861884 |
| comparative population genetic analysis of bocaccio rockfish sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci. | comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. the bocaccio rockfish sebastes paucispinis is a high gene-flow marine species off the west coast of north america that experienced strong population decline over the past 3 decades. we used 18 anonymous and 13 gene-associated simple sequence repeat (ssr) loci (expressed sequence tag [est]-ssrs) to characterize range-wide population structure with temporal ... | 2012 | 22490232 |
| discovery of the digirr gene from teleost fish: a novel toll-il-1 receptor family member serving as a negative regulator of il-1 signaling. | toll-il-1r (tir) family members play crucial roles in a variety of defense, inflammatory, injury, and stress responses. although they have been widely investigated in mammals, little is known about tirs in ancient vertebrates. in this study, we report a novel double ig il-1r related molecule (digirr) from three model fish (tetraodon nigroviridis, gasterosteus aculeatus, and takifugu rubripes), adding a previously unknown homolog to the tir family. this digirr molecule contains two ig-like domain ... | 2011 | 21804011 |
| developmental genetic basis for the evolution of pelvic fin loss in the pufferfish takifugu rubripes. | paired appendages were a key developmental innovation among vertebrates and they eventually evolved into limbs. ancient developmental control systems for paired fins and limbs are broadly conserved among gnathostome vertebrates. some lineages including whales, some salamanders, snakes, and many ray-fin fish, independently lost the pectoral, pelvic, or both appendages over evolutionary time. when different taxa independently evolve similar developmental morphologies, do they use the same molecula ... | 2005 | 15893975 |