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Hugues Roest Crollius - One of the best experts on this subject based on the ideXlab platform.
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Description of embryonic development of spotted green pufferfish (Tetraodon nigroviridis).
Zebrafish, 2014Co-Authors: Andreas Zaucker, Hugues Roest Crollius, Türker Bodur, Yavor Hadzhiev, Jochen Gehrig, Felix Loosli, Craig A. Watson, Ferenc MüllerAbstract: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 very limited utilization of pufferfish as an experimental model organism, due to the lack of established husbandry and developmental genetics protocols. In this study, we provide the first description of the normal embryonic development of Tetraodon nigroviridis. Embryos were obtained by in vitro fertilization of eggs, and subsequent development was monitored by brightfield microscopy at constant temperature. Tetraodon development was divided into distinct stages based on diagnostic morphological features, which were adopted from published literature on normal development of other fish species like medaka (Oryzias latipes), zebrafish (Danio rerio), and fugu. Tetraodon embryos show more similar morphologies to medaka than to zebrafish, reflecting its phylogenetic position. The early developmental stage series described in this study forms the foundation for the utilization of Tetraodon as an experimental model organism for comparative developmental studies.
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Description of Embryonic Development of Spotted Green Pufferfish (Tetraodon
2014Co-Authors: Andreas Zaucker, Hugues Roest Crollius, Yavor Hadzhiev, Jochen Gehrig, Felix Loosli, Ferenc MüllerAbstract: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 very limited utilization of pufferfish as an experimental model organism, due to the lack of established husbandry and developmental genetics protocols. In this study, we provide the first description of the normal embryonic development of Tetraodon nigroviridis. Embryos were obtained by in vitro fertilization of eggs, and subsequent development was monitored by brightfield microscopy at constant temperature. Tetraodon development was divided into distinct stages based on diagnostic morphological features, which were adopted from published literature on normal development of other fish species like medaka (Oryzias latipes), zebrafish (Danio rerio), and fugu. Tetraodon embryos show more similar morphologies to medaka than to zebrafish, reflecting its phylogenetic position. The early developmental stage series described in this study forms the foundation for the utilization of Tetraodon as an experimental model organism for comparative developmental studies.
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Reviews in Cell Biology and Molecular Medicine - Pufferfish Genomes: Takifugu and Tetraodon
Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2006Co-Authors: Melody S. Clark, Hugues Roest CrolliusAbstract:The pufferfish have some of the smallest vertebrate genomes known (350–500 Mb). This lead to two species, the Japanese pufferfish and the spotted green pufferfish ( Takifugu rubripes and Tetraodon nigroviridis respectively), being adopted as model vertebrates for in-depth genome-sequencing programs. These data have provided a wealth of information for comparative genomics studies in both fish and other vertebrate species, particularly human. This article describes the generalized features of the pufferfish genomes, the genome projects and resources available, in addition to the development of the pufferfish as genome tools. Keywords: Conserved Order; Conserved Segment; Conserved Synteny; Karyotype; Synteny; Takifugu; Tetraodon
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pufferfish genomes takifugu and Tetraodon
Reviews in Cell Biology and Molecular Medicine, 2006Co-Authors: Melody S. Clark, Hugues Roest CrolliusAbstract:The pufferfish have some of the smallest vertebrate genomes known (350–500 Mb). This lead to two species, the Japanese pufferfish and the spotted green pufferfish ( Takifugu rubripes and Tetraodon nigroviridis respectively), being adopted as model vertebrates for in-depth genome-sequencing programs. These data have provided a wealth of information for comparative genomics studies in both fish and other vertebrate species, particularly human. This article describes the generalized features of the pufferfish genomes, the genome projects and resources available, in addition to the development of the pufferfish as genome tools. Keywords: Conserved Order; Conserved Segment; Conserved Synteny; Karyotype; Synteny; Takifugu; Tetraodon
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Tetraodon poisson ou genome modele le poisson modele de recherche
Biofutur, 2005Co-Authors: Yann Esnault, Jean Weissenbach, Olivier Jaillon, Jeanmarc Aury, Hugues Roest CrolliusAbstract:Le principal attrait du poisson Tetraodon nigroviridis est son genome « compact », le plus petit connu parmi les vertebres. La comparaison de sa sequence avec celle du genome humain a permis d'evaluer le nombre des genes humains et d'ameliorer leur detection. A l'echelle chromosomique, elle a permis de reconstituer le caryotype du dernier ancetre commun a l'homme et aux poissons. Tout un pan de notre histoire evolutive est ainsi revele.
Chang Jen Huang - One of the best experts on this subject based on the ideXlab platform.
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Differential regulation of Tetraodon nigroviridis Mx gene promoter activity by constitutively-active forms of STAT1, STAT2, and IRF9.
Fish & shellfish immunology, 2014Co-Authors: Chia Hsiung Cheng, Chih Ming Chou, Cheng Ying Chu, Der Chen, Huang Wei Lien, Pung-pung Hwang, Mau-sun Chang, Chang Jen HuangAbstract:Induction of interferons (IFNs) produces an innate immune response through activation of the JAK-STAT signaling pathway. Type I IFN signaling activates downstream gene expression through the IFN-stimulated gene factor 3 (ISGF3) complex, while type II IFN (IFN-γ) signaling is mediated through active STAT1 protein. The IFN target gene Mx is involved in the defense against viral infection. However, the mechanism by which Tetraodon (pufferfish) Mx is regulated by IFN signaling has not been identified. In this study, we describe the cloning and expression of Tetraodon STAT1, STAT2, and IFN regulatory factor 9 (IRF9). By combining constitutively-active STAT1 (STAT1-JH1) and STAT2 (STA2-JH1) fusion proteins with IRF9, we demonstrate that a constitutively-active ISGF3 complex increases the transcriptional activity of the Tetraodon Mx promoter via direct binding to two IFN-stimulated response element (ISRE) sites. In addition, a constitutively-active TnIRF9-S2C containing a fusion of the C-terminal region of STAT2 and IRF9 also activated the Mx promoter through binding to the ISRE sites. Furthermore, constitutively-active STAT1-JH1 elevates Mx promoter activity through two IFN gamma-activated sequence (GAS) elements. The Mx promoter is also activated by constitutively-active TnIRF9-S2C and STAT1-JH1 protein, as determined using an in vivo luciferase assay. We conclude that the Tetraodon Mx gene is activated via Type I (IFN-1) and Type II (IFN-γ) signaling. These results provide mechanistic insights into the role of IFN signaling in teleosts, and the in vivo luciferase assay may be suitable as a tool for studying induction and regulation by IFNs in teleost fish.
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Genomic structure, expression and characterization of a STAT5 homologue from pufferfish (Tetraodon fluviatilis).
European journal of biochemistry, 2003Co-Authors: Shu Chiun Sung, Chih Ming Chou, Jiann-horng Leu, Ting Jia Fan, Ya Li Hsu, Shui Tsung Chen, Yueh Chun Hsieh, Chang Jen HuangAbstract:The STAT5 (signal transducer and activator of transcription 5) gene was isolated and characterized from a round-spotted pufferfish genomic library. This gene is composed of 19 exons spanning 11 kb. The full-length cDNA of Tetraodon fluviatilis STAT5 (TfSTAT5) contains 2461 bp and encodes a protein of 785 amino acid residues. From the amino acid sequence comparison, TfSTAT5 is most similar to mouse STAT5a and STAT5b with an overall identity of 76% and 78%, respectively, and has
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Isolation and identification of novel protein kinase genes from the round-spotted pufferfish (Tetraodon fluviatilis) genomic DNA.
Journal of biomedical science, 1998Co-Authors: Chih Ming Chou, Wen-chang Lin, Jiann-horng Leu, Chen-kung Chou, Chang Jen HuangAbstract:The round-spotted pufferfish Tetraodon fluviatilis has a genome size of 380 Mb which is slightly smaller than that of another pufferfish, Fugu rubripes rubripes (Fugu)
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Round-spotted pufferfish (Tetraodon fluviatilis) snf5 gene is oriented in a tail-to-tail manner with the set gene which encodes an inhibitor of protein phosphatase 2A.
DNA and cell biology, 1998Co-Authors: Chen-wen Yao, Chen-kung Chou, Jiann-horng Leu, Chuan Chin, Chang Jen HuangAbstract:The round-spotted pufferfish Tetraodon fluviatilis has a genome size of 380 Mb which is slightly smaller than that of another pufferfish Fugu rubripes rubripes (Fugu). Due to its compact genome and...
Olivier Jaillon - One of the best experts on this subject based on the ideXlab platform.
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Tetraodon poisson ou genome modele le poisson modele de recherche
Biofutur, 2005Co-Authors: Yann Esnault, Jean Weissenbach, Olivier Jaillon, Jeanmarc Aury, Hugues Roest CrolliusAbstract:Le principal attrait du poisson Tetraodon nigroviridis est son genome « compact », le plus petit connu parmi les vertebres. La comparaison de sa sequence avec celle du genome humain a permis d'evaluer le nombre des genes humains et d'ameliorer leur detection. A l'echelle chromosomique, elle a permis de reconstituer le caryotype du dernier ancetre commun a l'homme et aux poissons. Tout un pan de notre histoire evolutive est ainsi revele.
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genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto karyotype
Nature, 2004Co-Authors: Olivier Jaillon, Cécile Fischer, Laurence Bouneau, Jeanmarc Aury, Frederic Brunet, J R Petit, Nicole Stangethomann, Evan Mauceli, Catherine Ozoufcostaz, Alain BernotAbstract:Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests ∼900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
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comparative genomic analysis reveals independent expansion of a lineage specific gene family in vertebrates the class ii cytokine receptors and their ligands in mammals and fish
BMC Genomics, 2003Co-Authors: Georges Lutfalla, Hugues Roest Crollius, Olivier Jaillon, Nicole Stangethomann, Knud Erik Mogensen, Daniele MonneronAbstract:The high degree of sequence conservation between coding regions in fish and mammals can be exploited to identify genes in mammalian genomes by comparison with the sequence of similar genes in fish. Conversely, experimentally characterized mammalian genes may be used to annotate fish genomes. However, gene families that escape this principle include the rapidly diverging cytokines that regulate the immune system, and their receptors. A classic example is the class II helical cytokines (HCII) including type I, type II and lambda interferons, IL10 related cytokines (IL10, IL19, IL20, IL22, IL24 and IL26) and their receptors (HCRII). Despite the report of a near complete pufferfish (Takifugu rubripes) genome sequence, these genes remain undescribed in fish. We have used an original strategy based both on conserved amino acid sequence and gene structure to identify HCII and HCRII in the genome of another pufferfish, Tetraodon nigroviridis that is amenable to laboratory experiments. The 15 genes that were identified are highly divergent and include a single interferon molecule, three IL10 related cytokines and their potential receptors together with two Tissue Factor (TF). Some of these genes form tandem clusters on the Tetraodon genome. Their expression pattern was determined in different tissues. Most importantly, Tetraodon interferon was identified and we show that the recombinant protein can induce antiviral MX gene expression in Tetraodon primary kidney cells. Similar results were obtained in Zebrafish which has 7 MX genes. We propose a scheme for the evolution of HCII and their receptors during the radiation of bony vertebrates and suggest that the diversification that played an important role in the fine-tuning of the ancestral mechanism for host defense against infections probably followed different pathways in amniotes and fish.
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remarkable compartmentalization of transposable elements and pseudogenes in the heterochromatin of the Tetraodon nigroviridis genome
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Corinne Dasilva, Olivier Jaillon, Jean Weissenbach, Catherine Ozoufcostaz, Hajer Hadji, Sophie Nicaud, Hugues Roest CrolliusAbstract:Tetraodon nigroviridis is among the smallest known vertebrate genomes and as such represents an interesting model for studying genome architecture and evolution. Previous studies have shown that Tetraodon contains several types of tandem and dispersed repeats, but that their overall contribution is >10% of the genome. Using genomic library hybridization, fluorescent in situ hybridization, and whole genome shotgun and directed sequencing, we have investigated the global and local organization of repeat sequences in Tetraodon. We show that both tandem and dispersed repeat elements are compartmentalized in specific regions that correspond to the short arms of small subtelocentric chromosomes. The concentration of repeats in these heterochromatic regions is in sharp contrast to their paucity in euchromatin. In addition, we have identified a number of pseudogenes that have arisen through either duplication of genes or the retro-transcription of mRNAs. These pseudogenes are amplified to high numbers, some with more than 200 copies, and remain almost exclusively located in the same heterochromatic regions as transposable elements. The sequencing of one such heterochromatic region reveals a complex pattern of duplications and inversions, reminiscent of active and frequent rearrangements that can result in the truncation and hence inactivation of transposable elements. This tight compartmentalization of repeats and pseudogenes is absent in large vertebrate genomes such as mammals and is reminiscent of genomes that remain compact during evolution such as Drosophila and Arabidopsis.
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Four-hundred million years of conserved synteny of human Xp and Xq genes on three Tetraodon chromosomes.
Genome research, 2002Co-Authors: Frank Grützner, Hugues Roest Crollius, Olivier Jaillon, Jean Weissenbach, Götz Lütjens, Hans-hilger Ropers, Thomas HaafAbstract:The freshwater pufferfish Tetraodon nigroviridis (TNI) has become highly attractive as a compact reference vertebrate genome for gene finding and validation. We have mapped genes, which are more or less evenly spaced on the human chromosomes 9 and X, on Tetraodon chromosomes using fluorescence in situ hybridization (FISH), to establish syntenic relationships between Tetraodon and other key vertebrate genomes. PufferFISH revealed that the human X is an orthologous mosaic of three Tetraodon chromosomes. More than 350 million years ago, an ancestral vertebrate autosome shared orthologous Xp and Xq genes with Tetraodon chromosomes 1 and 7. The shuffled order of Xp and Xq orthologs on their syntenic Tetraodon chromosomes can be explained by the prevalence of evolutionary inversions. The Tetraodon 2 orthologous genes are clustered in human Xp11 and represent a recent addition to the eutherian X sex chromosome. The human chromosome 9 and the avian Z sex chromosome show a much lower degree of synteny conservation in the pufferfish than the human X chromosome. We propose that a special selection process during vertebrate evolution has shaped a highly conserved array(s) of X-linked genes long before the X was used as a mammalian sex chromosome and many X chromosomal genes were recruited for reproduction and/or the development of cognitive abilities. [Sequence data reported in this paper have been deposited in GenBank and assigned the following accession no: AJ308098.]
Haoran Lin - One of the best experts on this subject based on the ideXlab platform.
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Tetraodon nigroviridis: A model of Vibrio parahaemolyticus infection
Fish & shellfish immunology, 2016Co-Authors: Wan Peng, Yu Shi, Yaosi Liang, Yong Zhang, Li-bin Zhou, Haoran LinAbstract:Abstract Vibriosis is the most common bacterial diseases and brings great economic loss on aquaculture. Vibrio parahaemolyticus ( V. parahaemolyticus) , a gram-negative bacterium, has been identified as one main pathogens of Vibriosis. The pathogenic mechanism of V. parahaemolyticus is not entirely clear now. In our study, a model of V. parahaemolyticus infection of green-spotted puffer fish ( Tetraodon nigroviridis ) was established . T. nigroviridis were injected intraperitoneally (i.p.) with 200 μL of V. parahaemolyticus (8 × 10 10 CFU/mL). V. parahaemolyticus infection caused 64% mortality and infected some organs of T. nigroviridis . Histopathology studies revealed V. parahaemolyticus infection induced tissue structural changes, including adipose hollow space in the liver. Immunohistochemistry showed V. parahaemolyticus were present in infected tissue such as liver, head kidney and spleen. In livers of T. nigroviridis infected by V. parahaemolyticus , the alkaline phosphatases (ALP) activity first gradually increased and then backed to normal level, a trend that was on the contrary to the expression profile of the miR-29b. Quantitative real-time PCR analysis showed that the expression level of TLR1, TLR2, TLR5, TLR9, TLR21, NOD1, NOD2 and IL-6 in response to V. parahaemolyticus infection decreased compared to that of non-infected fish. The establishment of the T. nigroviridis model of V. parahaemolyticus infection further confirmed V. parahaemolyticus spreads through the blood circulation system primary as an extracellular pathogen. Meanwhile, liver is an important target organ when infected by V. parahaemolyticus . miR-29b in liver was involved in the progress of liver steatosis during V. parahaemolyticus infection. Moreover, V. parahaemolyticus infection in vivo may have an effect of immunosuppression on host.
Wan Peng - One of the best experts on this subject based on the ideXlab platform.
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Tetraodon nigroviridis: A model of Vibrio parahaemolyticus infection
Fish & shellfish immunology, 2016Co-Authors: Wan Peng, Yu Shi, Yaosi Liang, Yong Zhang, Li-bin Zhou, Haoran LinAbstract:Abstract Vibriosis is the most common bacterial diseases and brings great economic loss on aquaculture. Vibrio parahaemolyticus ( V. parahaemolyticus) , a gram-negative bacterium, has been identified as one main pathogens of Vibriosis. The pathogenic mechanism of V. parahaemolyticus is not entirely clear now. In our study, a model of V. parahaemolyticus infection of green-spotted puffer fish ( Tetraodon nigroviridis ) was established . T. nigroviridis were injected intraperitoneally (i.p.) with 200 μL of V. parahaemolyticus (8 × 10 10 CFU/mL). V. parahaemolyticus infection caused 64% mortality and infected some organs of T. nigroviridis . Histopathology studies revealed V. parahaemolyticus infection induced tissue structural changes, including adipose hollow space in the liver. Immunohistochemistry showed V. parahaemolyticus were present in infected tissue such as liver, head kidney and spleen. In livers of T. nigroviridis infected by V. parahaemolyticus , the alkaline phosphatases (ALP) activity first gradually increased and then backed to normal level, a trend that was on the contrary to the expression profile of the miR-29b. Quantitative real-time PCR analysis showed that the expression level of TLR1, TLR2, TLR5, TLR9, TLR21, NOD1, NOD2 and IL-6 in response to V. parahaemolyticus infection decreased compared to that of non-infected fish. The establishment of the T. nigroviridis model of V. parahaemolyticus infection further confirmed V. parahaemolyticus spreads through the blood circulation system primary as an extracellular pathogen. Meanwhile, liver is an important target organ when infected by V. parahaemolyticus . miR-29b in liver was involved in the progress of liver steatosis during V. parahaemolyticus infection. Moreover, V. parahaemolyticus infection in vivo may have an effect of immunosuppression on host.
