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Eric H. Davidson - One of the best experts on this subject based on the ideXlab platform.
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spbase the Sea Urchin genome database and web site
Nucleic Acids Research, 2009Co-Authors: Andrew R Cameron, Manoj P Samanta, Autumn Yuan, Dong He, Eric H. DavidsonAbstract:SpBase is a system of databases focused on the genomic information from Sea Urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful reSearch models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple Sea Urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple Sea Urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided.
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Sea Urchin forkhead gene family phylogeny and embryonic expression
Developmental Biology, 2006Co-Authors: Qiang Tu, Eric H. Davidson, Titus C Brown, Paola OliveriAbstract:Transcription factors of the Forkhead (Fox) family have been identified in many metazoans, and play important roles in diverse biological processes. Here we define the set of fox genes present in the Sea Urchin genome, and survey their usage during development. This genome includes 22 fox genes, only three of which were previously known. Of the 23 fox gene subclasses identified in vertebrate genomes, the Strongylocentrotus purpuratus genome has orthologues of all but four (E, H, R and S). Phylogenetic analysis suggests that one S. purpuratus fox gene is equally related to foxA and foxB of vertebrates; this gene defines a new class. Two other genes appear to be specific to the Sea Urchin, with respect to the genomes so far sequenced. Fox genes orthologous with those of vertebrates but lacking in arthropod or nematode genomes may be deuterostome-specific (subclasses I, J1, J2, L1, M and Q1), while the majority are pan-bilaterian. All but one of the S. purpuratus fox genes (SpfoxQ1) are expressed during embryogenesis, most in a very specific temporal and spatial manner. The Sea Urchin fox genes clearly execute many different regulatory functions, and almost all of them participate in the process of embryonic development.
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The Sea Urchin genome: Where will it lead us?
Science, 2006Co-Authors: Eric H. DavidsonAbstract:The Sea Urchin genome reveals large domains of biology heretofore unexplored at the genome level, as this is the first nonchordate deuterostome sequence. The sequence will accelerate progress toward complete understanding of the genomic regulatory system that controls developmental specification and morphogenetic function, thus illuminating basic developmental process in all animals.
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gene regulatory network controlling embryonic specification in the Sea Urchin
Current Opinion in Genetics & Development, 2004Co-Authors: Paola Oliveri, Eric H. DavidsonAbstract:The current state of the gene regulatory network for endomesoderm specification in Sea Urchin embryos is reviewed. The network was experimentally defined, and is presented as a predictive map of cis-regulatory inputs and functional regulatory gene interconnections (updated versions of the network and most of the underlying data are at http://sugp.caltech.edu/endomes/). The network illuminates the ‘whys’ of many aspects of zygotic control in early Sea Urchin development, both spatial and temporal. The network includes almost 50 genes, and these are organized in subcircuits, each of which executes a particular regulatory function.
Taku Hibino - One of the best experts on this subject based on the ideXlab platform.
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rtk and tgf β signaling pathways genes in the Sea Urchin genome
Developmental Biology, 2006Co-Authors: Francois Lapraz, Cynthia A. Bradham, Eric Rottinger, Veronique Duboc, Ryan Range, Louise Duloquin, Katherine D Walton, Shu Yu Wu, Mariano Loza, Taku HibinoAbstract:The Receptor Tyrosine kinase (RTK) and TGF-β signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding cytokines of the TGF-β superfamily and their downstream components. The Sea Urchin genome contains at least 20 genes coding for canonical receptor tyrosine kinases. Seventeen of the nineteen vertebrate RTK families are represented in the Sea Urchin. Fourteen of these RTK among which ALK, CCK4/PTK7, DDR, EGFR, EPH, LMR, MET/RON, MUSK, RET, ROR, ROS, RYK, TIE and TRK are present as single copy genes while pairs of related genes are present for VEGFR, FGFR and INSR. Similarly, nearly all the subfamilies of TGF-β ligands identified in vertebrates are present in the Sea Urchin genome including the BMP, ADMP, GDF, Activin, Myostatin, Nodal and Lefty, as well as the TGF-β sensu stricto that had not been characterized in invertebrates so far. Expression analysis indicates that the early expression of nodal, BMP2/4 and lefty is restricted to the oral ectoderm reflecting their role in providing positional information along the oral–aboral axis of the embryo. The coincidence between the emergence of TGF-β-related factors such as Nodal and Lefty and the emergence of the deuterostome lineage strongly suggests that the ancestral function of Nodal could have been related to the secondary opening of the mouth which characterizes this clade, a hypothesis supported by functional data in the extant species. The Sea Urchin genome contains 6 genes encoding TGF-β receptors and 4 genes encoding prototypical Smad proteins. Furthermore, most of the transcriptional activatorsandrepressorsshowntointeractwithSmadsinvertebrates haveorthologuesinechinoderms.Finally,theSeaUrchingenome contains an almost complete repertoire of genes encoding extracellular modulators of BMP signaling including Chordin, Noggin, Sclerotin, SFRP, Gremlin, DAN and Twisted gastrulation. Taken together, these findings indicate that the Sea Urchin complement of genes of the RTK and TGF-β signaling pathways is qualitatively very similar to the repertoire present in vertebrates, and that these genes are part of the common genetool kit for intercellular signaling of deuterostomes. © 2006 Elsevier Inc. All rights reserved.
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genomic insights into the immune system of the Sea Urchin
Science, 2006Co-Authors: Jonathan P. Rast, Taku Hibino, Courtney L Smith, Mariano Lozacoll, Gary W LitmanAbstract:Comparative analysis of the Sea Urchin genome has broad implications for the primitive state of deuterostome host defense and the genetic underpinnings of immunity in vertebrates. The Sea Urchin has an unprecedented complexity of innate immune recognition receptors relative to other animal species yet characterized. These receptor genes include a vast repertoire of 222 Toll-like receptors, a superfamily of more than 200 NACHT domain-leucine-rich repeat proteins (similar to nucleotide-binding and oligomerization domain (NOD) and NALP proteins of vertebrates), and a large family of scavenger receptor cysteine-rich proteins. More typical numbers of genes encode other immune recognition factors. Homologs of important immune and hematopoietic regulators, many of which have previously been identified only from chordates, as well as genes that are critical in adaptive immunity of jawed vertebrates, also are present. The findings serve to underscore the dynamic utilization of receptors and the complexity of immune recognition that may be basal for deuterostomes and predicts features of the ancestral bilaterian form.
Maria I. Arnone - One of the best experts on this subject based on the ideXlab platform.
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unique system of photoreceptors in Sea Urchin tube feet
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Esther Ullrichluter, Sam Dupont, Enrique Arboleda, Harald Zur Hausen, Maria I. ArnoneAbstract:Different Sea Urchin species show a vast variety of responses to variations in light intensity; however, despite this behavioral evidence for photosensitivity, light sensing in these animals has remained an enigma. Genome information of the recently sequenced purple Sea Urchin (Strongylocentrotus purpuratus) allowed us to address this question from a previously unexplored molecular perspective by localizing expression of the rhabdomeric opsin Sp-opsin4 and Sp-pax6, two genes essential for photoreceptor function and development, respectively. Using a specifically designed antibody against Sp-Opsin4 and in situ hybridization for both genes, we detected expression in two distinct groups of photoreceptor cells (PRCs) located in the animal's numerous tube feet. Specific reactivity of the Sp-Opsin4 antibody with Sea star optic cushions, which regulate phototaxis, suggests a similar visual function in Sea Urchins. Ultrastructural characterization of the Sea Urchin PRCs revealed them to be of a microvillar receptor type. Our data suggest that echinoderms, in contrast to chordates, deploy a microvillar, r-opsin–expressing PRC type for vision, a feature that has been so far documented only in protostome animals. Surprisingly, Sea Urchin PRCs lack any associated screening pigment. Indeed, one of the tube foot PRC clusters may account for directional vision by being shaded through the opaque calcite skeleton. The PRC axons connect to the animal internal nervous system, suggesting an integrative function beyond local short circuits. Because juveniles display no phototaxis until skeleton completion, we suggest a model in which the entire Sea Urchin, deploying its skeleton as PRC screening device, functions as a huge compound eye.
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opsins and clusters of sensory g protein coupled receptors in the Sea Urchin genome
Developmental Biology, 2006Co-Authors: Florian Raible, Enrique Arboleda, Kristin Tessmarraible, Tobias Kaller, Peer Bork, Detlev Arendt, Maria I. ArnoneAbstract:Rhodopsin-type G-protein-coupled receptors (GPCRs) contribute the majority of sensory receptors in vertebrates. With 979 members, they form the largest GPCR family in the sequenced Sea Urchin genome, constituting more than 3% of all predicted genes. The Sea Urchin genome encodes at least six Opsin proteins. Of these, one rhabdomeric, one ciliary and two Go-type Opsins can be assigned to ancient bilaterian Opsin subfamilies. Moreover, we identified four greatly expanded subfamilies of rhodopsin-type GPCRs that we call Sea Urchin specific rapidly expanded lineages of GPCRs (surreal-GPCRs). Our analysis of two of these groups revealed genomic clustering and single-exon gene structures similar to the most expanded group of vertebrate rhodopsin-type GPCRs, the olfactory receptors. We hypothesize that these genes arose by rapid duplication in the echinoid lineage and act as chemosensory receptors of the animal. In support of this, group B surreal-GPCRs are most prominently expressed in distinct classes of pedicellariae and tube feet of the adult Sea Urchin, structures that have previously been shown to react to chemical stimuli and to harbor sensory neurons in echinoderms. Notably, these structures also express different opsins, indicating that Sea Urchins possess an intricate molecular set-up to sense their environment.
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The Sea Urchin kinome: a first look.
Developmental Biology, 2006Co-Authors: Cynthia A. Bradham, Julia Morales, Kathy R. Foltz, Wendy S. Beane, Maria I. Arnone, Francesca Rizzo, James A. Coffman, Arcady Mushegian, Manisha Goel, Anne Marie GenevièreAbstract:This paper reports a preliminary in silico analysis of the Sea Urchin kinome. The predicted protein kinases in the Sea Urchin genome were identified, annotated and classified, according to both function and kinase domain taxonomy. The results show that the Sea Urchin kinome, consisting of 353 protein kinases, is closer to the Drosophila kinome (239) than the human kinome (518) with respect to total kinase number. However, the diversity of Sea Urchin kinases is surprisingly similar to humans, since the Urchin kinome is missing only 4 of 186 human subfamilies, while Drosophila lacks 24. Thus, the Sea Urchin kinome combines the simplicity of a non-duplicated genome with the diversity of function and signaling previously considered to be vertebrate-specific. More than half of the Sea Urchin kinases are involved with signal transduction, and approximately 88% of the signaling kinases are expressed in the developing embryo. These results support the strength of this nonchordate deuterostome as a pivotal developmental and evolutionary model organism.
Veronique Duboc - One of the best experts on this subject based on the ideXlab platform.
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rtk and tgf β signaling pathways genes in the Sea Urchin genome
Developmental Biology, 2006Co-Authors: Francois Lapraz, Cynthia A. Bradham, Eric Rottinger, Veronique Duboc, Ryan Range, Louise Duloquin, Katherine D Walton, Shu Yu Wu, Mariano Loza, Taku HibinoAbstract:The Receptor Tyrosine kinase (RTK) and TGF-β signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding cytokines of the TGF-β superfamily and their downstream components. The Sea Urchin genome contains at least 20 genes coding for canonical receptor tyrosine kinases. Seventeen of the nineteen vertebrate RTK families are represented in the Sea Urchin. Fourteen of these RTK among which ALK, CCK4/PTK7, DDR, EGFR, EPH, LMR, MET/RON, MUSK, RET, ROR, ROS, RYK, TIE and TRK are present as single copy genes while pairs of related genes are present for VEGFR, FGFR and INSR. Similarly, nearly all the subfamilies of TGF-β ligands identified in vertebrates are present in the Sea Urchin genome including the BMP, ADMP, GDF, Activin, Myostatin, Nodal and Lefty, as well as the TGF-β sensu stricto that had not been characterized in invertebrates so far. Expression analysis indicates that the early expression of nodal, BMP2/4 and lefty is restricted to the oral ectoderm reflecting their role in providing positional information along the oral–aboral axis of the embryo. The coincidence between the emergence of TGF-β-related factors such as Nodal and Lefty and the emergence of the deuterostome lineage strongly suggests that the ancestral function of Nodal could have been related to the secondary opening of the mouth which characterizes this clade, a hypothesis supported by functional data in the extant species. The Sea Urchin genome contains 6 genes encoding TGF-β receptors and 4 genes encoding prototypical Smad proteins. Furthermore, most of the transcriptional activatorsandrepressorsshowntointeractwithSmadsinvertebrates haveorthologuesinechinoderms.Finally,theSeaUrchingenome contains an almost complete repertoire of genes encoding extracellular modulators of BMP signaling including Chordin, Noggin, Sclerotin, SFRP, Gremlin, DAN and Twisted gastrulation. Taken together, these findings indicate that the Sea Urchin complement of genes of the RTK and TGF-β signaling pathways is qualitatively very similar to the repertoire present in vertebrates, and that these genes are part of the common genetool kit for intercellular signaling of deuterostomes. © 2006 Elsevier Inc. All rights reserved.
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nodal and bmp2 4 signaling organizes the oral aboral axis of the Sea Urchin embryo
Developmental Cell, 2004Co-Authors: Veronique Duboc, Eric Rottinger, Lydia Besnardeau, Thierry LepageAbstract:Abstract In the Sea Urchin embryo, the oral-aboral axis is specified after fertilization by mechanisms that are largely unknown. We report that early Sea Urchin embryos express Nodal and Antivin in the presumptive oral ectoderm and demonstrate that these genes control formation of the oral-aboral axis. Overexpression of nodal converted the whole ectoderm into oral ectoderm and induced ectopic expression of the orally expressed genes goosecoid , brachyury , BMP2/4 , and antivin . Conversely, when the function of Nodal was blocked, by injection of an antisense Morpholino oligonucleotide or by injection of antivin mRNA, neither the oral nor the aboral ectoderm were specified. Injection of nodal mRNA into Nodal-deficient embryos induced an oral-aboral axis in a largely non-cell-autonomous manner. These observations suggest that the mechanisms responsible for patterning the oral-aboral axis of the Sea Urchin embryo may share similarities with mechanisms that pattern the dorsoventral axis of other deuterostomes.
Eric Rottinger - One of the best experts on this subject based on the ideXlab platform.
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rtk and tgf β signaling pathways genes in the Sea Urchin genome
Developmental Biology, 2006Co-Authors: Francois Lapraz, Cynthia A. Bradham, Eric Rottinger, Veronique Duboc, Ryan Range, Louise Duloquin, Katherine D Walton, Shu Yu Wu, Mariano Loza, Taku HibinoAbstract:The Receptor Tyrosine kinase (RTK) and TGF-β signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding cytokines of the TGF-β superfamily and their downstream components. The Sea Urchin genome contains at least 20 genes coding for canonical receptor tyrosine kinases. Seventeen of the nineteen vertebrate RTK families are represented in the Sea Urchin. Fourteen of these RTK among which ALK, CCK4/PTK7, DDR, EGFR, EPH, LMR, MET/RON, MUSK, RET, ROR, ROS, RYK, TIE and TRK are present as single copy genes while pairs of related genes are present for VEGFR, FGFR and INSR. Similarly, nearly all the subfamilies of TGF-β ligands identified in vertebrates are present in the Sea Urchin genome including the BMP, ADMP, GDF, Activin, Myostatin, Nodal and Lefty, as well as the TGF-β sensu stricto that had not been characterized in invertebrates so far. Expression analysis indicates that the early expression of nodal, BMP2/4 and lefty is restricted to the oral ectoderm reflecting their role in providing positional information along the oral–aboral axis of the embryo. The coincidence between the emergence of TGF-β-related factors such as Nodal and Lefty and the emergence of the deuterostome lineage strongly suggests that the ancestral function of Nodal could have been related to the secondary opening of the mouth which characterizes this clade, a hypothesis supported by functional data in the extant species. The Sea Urchin genome contains 6 genes encoding TGF-β receptors and 4 genes encoding prototypical Smad proteins. Furthermore, most of the transcriptional activatorsandrepressorsshowntointeractwithSmadsinvertebrates haveorthologuesinechinoderms.Finally,theSeaUrchingenome contains an almost complete repertoire of genes encoding extracellular modulators of BMP signaling including Chordin, Noggin, Sclerotin, SFRP, Gremlin, DAN and Twisted gastrulation. Taken together, these findings indicate that the Sea Urchin complement of genes of the RTK and TGF-β signaling pathways is qualitatively very similar to the repertoire present in vertebrates, and that these genes are part of the common genetool kit for intercellular signaling of deuterostomes. © 2006 Elsevier Inc. All rights reserved.
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nodal and bmp2 4 signaling organizes the oral aboral axis of the Sea Urchin embryo
Developmental Cell, 2004Co-Authors: Veronique Duboc, Eric Rottinger, Lydia Besnardeau, Thierry LepageAbstract:Abstract In the Sea Urchin embryo, the oral-aboral axis is specified after fertilization by mechanisms that are largely unknown. We report that early Sea Urchin embryos express Nodal and Antivin in the presumptive oral ectoderm and demonstrate that these genes control formation of the oral-aboral axis. Overexpression of nodal converted the whole ectoderm into oral ectoderm and induced ectopic expression of the orally expressed genes goosecoid , brachyury , BMP2/4 , and antivin . Conversely, when the function of Nodal was blocked, by injection of an antisense Morpholino oligonucleotide or by injection of antivin mRNA, neither the oral nor the aboral ectoderm were specified. Injection of nodal mRNA into Nodal-deficient embryos induced an oral-aboral axis in a largely non-cell-autonomous manner. These observations suggest that the mechanisms responsible for patterning the oral-aboral axis of the Sea Urchin embryo may share similarities with mechanisms that pattern the dorsoventral axis of other deuterostomes.
