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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 ...200717374158
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 ...200717468028
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 ...200717497430
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 ...200717570761
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 ...200717632107
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 ...200717717047
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 ...200717873000
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 ...200717932072
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 ...200717936743
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 ...200717940200
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 ...200717950621
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 ...200817950734
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 ...200817973185
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 ...200818029016
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 ...200818070106
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) ...200818164212
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 ...200818191858
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 ...200418248232
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 ...200818261720
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 ...200818262266
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 ...200818266867
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.200818298844
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 ...200818343608
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 ...200818372402
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 ...200818452704
early vertebrate chromosome duplications and the evolution of the neuropeptide y receptor gene regions.one of the many gene families that expanded in early vertebrate evolution is the neuropeptide (npy) receptor family of g-protein coupled receptors. earlier work by our lab suggested that several of the npy receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes) and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. in this study we ha ...200818578868
genomic characterization and tissue distribution of leptin receptor and leptin receptor overlapping transcript genes in the pufferfish, takifugu rubripes.full-length cdnas encoding the leptin receptor (tflepr), leptin receptor overlapping transcript (tfleprot) and leptin receptor overlapping transcript-like 1 (tfleprotl1) were cloned and sequenced from the pufferfish, takifugurubripes. the tflepr gene encoded an 1116-amino acid protein that includes almost all functionally important domains conserved among vertebrate lepr such as three fibronectin type iii domains, the immunoglobulin (ig) c2-like domain and a pair of repeated tryptophan/serine mo ...200818582469
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 ...200318629122
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 ...200818714020
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 ...200818803835
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 ...200919022503
[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 ...200819073576
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. ...200919091910
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 ...200819116084
codon usage bias is correlated with gene expression levels in the fission yeast schizosaccharomyces pombe.usage of synonymous codons represents a characteristic pattern of preference in each organism. it has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. here we examined synonymous codon usage in genes of the fission yeast schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. in this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most o ...200919335619
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 ...200819506737
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 ...200919778249
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 ...201019778549
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 ...200919949461
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 ...201020034105
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 ...201020144719
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 ...201020146379
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 ...200920198186
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 ...201020383527
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 ...200620483231
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 ...200620483233
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 ...200620483234
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 ...200620483241
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 ...200620483243
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 ...200620483246
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.201020569428
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 ...201020591844
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 ...201020637221
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 ...201020726939
first molluscan transcription factor activator protein-1 (ap-1) member from disk abalone and its expression profiling against immune challenge and tissue injury.the regulation of transcriptional activation is an essential and critical point in gene expression. in this study, we describe a novel transcription factor activator protein-1 (ap-1) gene from disk abalone haliotis discus discus (abap-1) for the first time in mollusk. it was identified by homology screening of an abalone normalized cdna library. the cloned abap-1 consists of a 945 bp coding region that encodes a putative protein containing 315 amino acids. the abap-1 gene is composed of a charac ...201020732431
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 ...201121268182
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 ...201121342560
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 ...201121416149
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 ...201121466417
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 ...201121551351
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 ...201121620332
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 ...200821798149
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 ...201021798198
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 ...201121804011
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 ...201121884110
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 ...201221898790
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 ...201121947600
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 ...201122073989
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 ...201122107841
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 ...201122120661
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 ...201122155550
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 ...201222266137
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 ...201222490232
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 ...201222579469
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 ...201222803724
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 ...201322843312
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 ...201323422813
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 ...201323521844
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 ...201323562572
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 ( ...201323769874
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 ...201323867289
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 ...201323872522
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 ...201324059862
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 ...201324225309
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 ...201424392850
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 ...201424440488
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. ...201424561126
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 ...201525128157
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 ...201425199543
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 ...201425243591
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 ...201525458310
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 ...201525842264
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 ...201525871516
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 ...201526162478
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 ...201626472618
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 ...201526535692
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 ...201626777033
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 ...201627514788
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 ...201728286257
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