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  • 1
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    A genomic regulatory network for development (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-03-02
    Description: Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- Rast, Jonathan P -- Oliveri, Paola -- Ransick, Andrew -- Calestani, Cristina -- Yuh, Chiou-Hwa -- Minokawa, Takuya -- Amore, Gabriele -- Hinman, Veronica -- Arenas-Mena, Cesar -- Otim, Ochan -- Brown, C Titus -- Livi, Carolina B -- Lee, Pei Yun -- Revilla, Roger -- Rust, Alistair G -- Pan, Zheng jun -- Schilstra, Maria J -- Clarke, Peter J C -- Arnone, Maria I -- Rowen, Lee -- Cameron, R Andrew -- McClay, David R -- Hood, Leroy -- Bolouri, Hamid -- GM-61005/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- RR-06591/RR/NCRR NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2002 Mar 1;295(5560):1669-78.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11872831" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Lineage ; Computational Biology ; Embryonic Development ; Endoderm/cytology/*physiology ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genes, Regulator ; *Genome ; Mesoderm/cytology/*physiology ; Models, Biological ; Models, Genetic ; Morphogenesis ; Regulatory Sequences, Nucleic Acid ; Sea Urchins/*embryology/*genetics ; Stem Cells/physiology ; Systems Theory
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-04-16
    Description: The genomic regulatory network that controls gene expression ultimately determines form and function in each species. The operational nature of the regulatory programming specified in cis-regulatory DNA sequence was determined from a detailed functional analysis of a sea urchin control element that directs the expression of a gene in the endoderm during development. Spatial expression and repression, and the changing rate of transcription of this gene, are mediated by a complex and extended cis-regulatory system. The system may be typical of developmental cis-regulatory apparatus. All of its activities are integrated in the proximal element, which contains seven target sites for DNA binding proteins. A quantitative computational model of this regulatory element was constructed that explicitly reveals the logical interrelations hard-wired into the DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yuh, C H -- Bolouri, H -- Davidson, E H -- New York, N.Y. -- Science. 1998 Mar 20;279(5358):1896-902.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9506933" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Cell Adhesion Molecules/*genetics/physiology ; Computer Simulation ; DNA-Binding Proteins/metabolism ; Embryo, Nonmammalian/metabolism ; Endoderm/metabolism ; Gastrula/metabolism ; *Gene Expression Regulation, Developmental ; Lithium Chloride/pharmacology ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis ; Promoter Regions, Genetic/genetics/*physiology ; Proteins/*genetics/physiology ; Sea Urchins/embryology/*genetics/metabolism ; *Transcription, Genetic/drug effects
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    The sea urchin genome: where will it lead us? (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):939-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095689" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; Embryo, Nonmammalian/physiology ; Embryonic Development ; Gene Expression Regulation ; Genes, Regulator ; Genetic Speciation ; *Genome ; Genomics ; Male ; Morphogenesis ; Sequence Analysis, DNA ; Strongylocentrotus purpuratus/embryology/*genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Gene regulatory networks and the evolution of animal body plans (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: Development of the animal body plan is controlled by large gene regulatory networks (GRNs), and hence evolution of body plans must depend upon change in the architecture of developmental GRNs. However, these networks are composed of diverse components that evolve at different rates and in different ways. Because of the hierarchical organization of developmental GRNs, some kinds of change affect terminal properties of the body plan such as occur in speciation, whereas others affect major aspects of body plan morphology. A notable feature of the paleontological record of animal evolution is the establishment by the Early "Cambrian of virtually all phylum-level body plans. We identify a class of GRN component, the kernels" of the network, which, because of their developmental role and their particular internal structure, are most impervious to change. Conservation of phyletic body plans may have been due to the retention since pre-Cambrian time of GRN kernels, which underlie development of major body parts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- Erwin, Douglas H -- HD37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):796-800.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469913" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological/genetics ; Animals ; *Biological Evolution ; Body Patterning/*genetics ; Embryonic Development ; Fossils ; *Gene Expression Regulation, Developmental ; Genes, Regulator ; Genetic Speciation ; Morphogenesis/*genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    The transcriptome of the sea urchin embryo (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Samanta, Manoj P -- Tongprasit, Waraporn -- Istrail, Sorin -- Cameron, R Andrew -- Tu, Qiang -- Davidson, Eric H -- Stolc, Viktor -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):960-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Systemix Institute, Los Altos, CA 94024, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095694" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Blastula/metabolism ; Computational Biology ; Embryo, Nonmammalian/*metabolism ; Embryonic Development/*genetics ; Gastrula/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; *Genome ; Intracellular Signaling Peptides and Proteins/genetics/metabolism ; Molecular Probe Techniques ; Nucleic Acid Hybridization ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/genetics/metabolism ; RNA, Untranslated/genetics/metabolism ; Signal Transduction/genetics ; Strongylocentrotus purpuratus/*embryology/*genetics/growth & development ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Phosphatized polar lobe-forming embryos from the Precambrian of southwest China (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-17
    Description: In developing embryos of some extant spiralian animals, polar lobe formation is one of the symmetry-breaking mechanisms for segregation of maternal cytoplasmic substances to certain blastomeres and not others. Polar lobe formation leads to unique early cleavage morphologies that include trilobed, J-shaped, and five-lobed structures. Fossil embryos similar to modern lobeforming embryos are recognized from the Precambrian Doushantuo Formation phosphates, Weng'an, Guizhou Province, China. These embryos are abundant and form a developmental sequence comparable to different developing stages observed in lobe-forming embryos of extant spiralians. These data imply that lobe formation is an evolutionarily ancient process of embryonic specification.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Jun-Yuan -- Bottjer, David J -- Davidson, Eric H -- Dornbos, Stephen Q -- Gao, Xiang -- Yang, Yong-Hua -- Li, Chia-Wei -- Li, Gang -- Wang, Xiu-Qiang -- Xian, Ding-Chang -- Wu, Hung-Jen -- Hwu, Yeu-Kuang -- Tafforeau, Paul -- New York, N.Y. -- Science. 2006 Jun 16;312(5780):1644-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nanjing Institute of Geology and Paleontology, Institute of Evo/Developmental Biology, and State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China. chenjy@nju.edu.cn〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16778054" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Annelida/embryology ; Biological Evolution ; Blastomeres/cytology ; China ; Embryo, Nonmammalian/*anatomy & histology/cytology ; *Embryonic Development ; *Fossils ; Geologic Sediments ; Invertebrates/*embryology ; Mollusca/embryology ; Phosphates ; Platyhelminths/embryology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 7
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    A gene regulatory network subcircuit drives a dynamic pattern of gene expression (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-03
    Description: Early specification of endomesodermal territories in the sea urchin embryo depends on a moving torus of regulatory gene expression. We show how this dynamic patterning function is encoded in a gene regulatory network (GRN) subcircuit that includes the otx, wnt8, and blimp1 genes, the cis-regulatory control systems of which have all been experimentally defined. A cis-regulatory reconstruction experiment revealed that blimp1 autorepression accounts for progressive extinction of expression in the center of the torus, whereas its outward expansion follows reception of the Wnt8 ligand by adjacent cells. GRN circuitry thus controls not only static spatial assignment in development but also dynamic regulatory patterning.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Joel -- Theodoris, Christina -- Davidson, Eric H -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):794-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, 156-29, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17975065" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; *Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; Male ; Sea Urchins/*genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Development. Built to run, not fail (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oliveri, Paola -- Davidson, Eric H -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 16;315(5818):1510-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. poliveri@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17363653" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Embryonic Development/*genetics ; *Gene Regulatory Networks ; Genes, Regulator ; Repressor Proteins/genetics/metabolism ; Signal Transduction ; Transcription Factors/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Retrospective. Roy J. Britten (1919-2012) (2012)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2012-03-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Davidson, Eric H -- New York, N.Y. -- Science. 2012 Mar 9;335(6073):1183. doi: 10.1126/science.1220828.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22403381" target="_blank"〉PubMed〈/a〉
    Keywords: DNA/chemistry ; Evolution, Molecular ; Gene Expression Regulation ; Genomics/history ; History, 20th Century ; History, 21st Century ; Molecular Biology/*history ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Small bilaterian fossils from 40 to 55 million years before the cambrian (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-06-05
    Description: Ten phosphatized specimens of a small (〈180 micrometers) animal displaying clear bilaterian features have been recovered from the Doushantuo Formation, China, dating from 40 to 55 million years before the Cambrian. Seen in sections, this animal (Vernanimalcula guizhouena gen. et sp. nov.) had paired coeloms extending the length of the gut; paired external pits that could be sense organs; bilateral, anterior-posterior organization; a ventrally directed anterior mouth with thick walled pharynx; and a triploblastic structure. The structural complexity is that of an adult rather than a larval form. These fossils provide the first evidence confirming the phylogenetic inference that Bilateria arose well before the Cambrian.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Jun-Yuan -- Bottjer, David J -- Oliveri, Paola -- Dornbos, Stephen Q -- Gao, Feng -- Ruffins, Seth -- Chi, Huimei -- Li, Chia-Wei -- Davidson, Eric H -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):218-22. Epub 2004 Jun 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Nanjing Institute of Geology and Paleontology, Nanjing 210008, China. chenjunyuan@163.net〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15178752" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Evolution ; China ; Digestive System/anatomy & histology ; Endoderm ; *Fossils ; *Invertebrates/anatomy & histology/classification ; Mesoderm ; Phylogeny ; Time
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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