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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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    The genome of the sea urchin Strongylocentrotus purpuratus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sea Urchin Genome Sequencing Consortium -- Sodergren, Erica -- Weinstock, George M -- Davidson, Eric H -- Cameron, R Andrew -- Gibbs, Richard A -- Angerer, Robert C -- Angerer, Lynne M -- Arnone, Maria Ina -- Burgess, David R -- Burke, Robert D -- Coffman, James A -- Dean, Michael -- Elphick, Maurice R -- Ettensohn, Charles A -- Foltz, Kathy R -- Hamdoun, Amro -- Hynes, Richard O -- Klein, William H -- Marzluff, William -- McClay, David R -- Morris, Robert L -- Mushegian, Arcady -- Rast, Jonathan P -- Smith, L Courtney -- Thorndyke, Michael C -- Vacquier, Victor D -- Wessel, Gary M -- Wray, Greg -- Zhang, Lan -- Elsik, Christine G -- Ermolaeva, Olga -- Hlavina, Wratko -- Hofmann, Gretchen -- Kitts, Paul -- Landrum, Melissa J -- Mackey, Aaron J -- Maglott, Donna -- Panopoulou, Georgia -- Poustka, Albert J -- Pruitt, Kim -- Sapojnikov, Victor -- Song, Xingzhi -- Souvorov, Alexandre -- Solovyev, Victor -- Wei, Zheng -- Whittaker, Charles A -- Worley, Kim -- Durbin, K James -- Shen, Yufeng -- Fedrigo, Olivier -- Garfield, David -- Haygood, Ralph -- Primus, Alexander -- Satija, Rahul -- Severson, Tonya -- Gonzalez-Garay, Manuel L -- Jackson, Andrew R -- Milosavljevic, Aleksandar -- Tong, Mark -- Killian, Christopher E -- Livingston, Brian T -- Wilt, Fred H -- Adams, Nikki -- Belle, Robert -- Carbonneau, Seth -- Cheung, Rocky -- Cormier, Patrick -- Cosson, Bertrand -- Croce, Jenifer -- Fernandez-Guerra, Antonio -- Geneviere, Anne-Marie -- Goel, Manisha -- Kelkar, Hemant -- Morales, Julia -- Mulner-Lorillon, Odile -- Robertson, Anthony J -- Goldstone, Jared V -- Cole, Bryan -- Epel, David -- Gold, Bert -- Hahn, Mark E -- Howard-Ashby, Meredith -- Scally, Mark -- Stegeman, John J -- Allgood, Erin L -- Cool, Jonah -- Judkins, Kyle M -- McCafferty, Shawn S -- Musante, Ashlan M -- Obar, Robert A -- Rawson, Amanda P -- Rossetti, Blair J -- Gibbons, Ian R -- Hoffman, Matthew P -- Leone, Andrew -- Istrail, Sorin -- Materna, Stefan C -- Samanta, Manoj P -- Stolc, Viktor -- Tongprasit, Waraporn -- Tu, Qiang -- Bergeron, Karl-Frederik -- Brandhorst, Bruce P -- Whittle, James -- Berney, Kevin -- Bottjer, David J -- Calestani, Cristina -- Peterson, Kevin -- Chow, Elly -- Yuan, Qiu Autumn -- Elhaik, Eran -- Graur, Dan -- Reese, Justin T -- Bosdet, Ian -- Heesun, Shin -- Marra, Marco A -- Schein, Jacqueline -- Anderson, Michele K -- Brockton, Virginia -- Buckley, Katherine M -- Cohen, Avis H -- Fugmann, Sebastian D -- Hibino, Taku -- Loza-Coll, Mariano -- Majeske, Audrey J -- Messier, Cynthia -- Nair, Sham V -- Pancer, Zeev -- Terwilliger, David P -- Agca, Cavit -- Arboleda, Enrique -- Chen, Nansheng -- Churcher, Allison M -- Hallbook, F -- Humphrey, Glen W -- Idris, Mohammed M -- Kiyama, Takae -- Liang, Shuguang -- Mellott, Dan -- Mu, Xiuqian -- Murray, Greg -- Olinski, Robert P -- Raible, Florian -- Rowe, Matthew -- Taylor, John S -- Tessmar-Raible, Kristin -- Wang, D -- Wilson, Karen H -- Yaguchi, Shunsuke -- Gaasterland, Terry -- Galindo, Blanca E -- Gunaratne, Herath J -- Juliano, Celina -- Kinukawa, Masashi -- Moy, Gary W -- Neill, Anna T -- Nomura, Mamoru -- Raisch, Michael -- Reade, Anna -- Roux, Michelle M -- Song, Jia L -- Su, Yi-Hsien -- Townley, Ian K -- Voronina, Ekaterina -- Wong, Julian L -- Amore, Gabriele -- Branno, Margherita -- Brown, Euan R -- Cavalieri, Vincenzo -- Duboc, Veronique -- Duloquin, Louise -- Flytzanis, Constantin -- Gache, Christian -- Lapraz, Francois -- Lepage, Thierry -- Locascio, Annamaria -- Martinez, Pedro -- Matassi, Giorgio -- Matranga, Valeria -- Range, Ryan -- Rizzo, Francesca -- Rottinger, Eric -- Beane, Wendy -- Bradham, Cynthia -- Byrum, Christine -- Glenn, Tom -- Hussain, Sofia -- Manning, Gerard -- Miranda, Esther -- Thomason, Rebecca -- Walton, Katherine -- Wikramanayke, Athula -- Wu, Shu-Yu -- Xu, Ronghui -- Brown, C Titus -- Chen, Lili -- Gray, Rachel F -- Lee, Pei Yun -- Nam, Jongmin -- Oliveri, Paola -- Smith, Joel -- Muzny, Donna -- Bell, Stephanie -- Chacko, Joseph -- Cree, Andrew -- Curry, Stacey -- Davis, Clay -- Dinh, Huyen -- Dugan-Rocha, Shannon -- Fowler, Jerry -- Gill, Rachel -- Hamilton, Cerrissa -- Hernandez, Judith -- Hines, Sandra -- Hume, Jennifer -- Jackson, Laronda -- Jolivet, Angela -- Kovar, Christie -- Lee, Sandra -- Lewis, Lora -- Miner, George -- Morgan, Margaret -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Parker, David -- Pu, Ling-Ling -- Thorn, Rachel -- Wright, Rita -- 2P42 ESO7381/PHS HHS/ -- 5 U54 HG003273/HG/NHGRI NIH HHS/ -- EY11930/EY/NEI NIH HHS/ -- F32 ESO12794/PHS HHS/ -- F32 HD047136/HD/NICHD NIH HHS/ -- F32 HD047136-02/HD/NICHD NIH HHS/ -- F32 HD047136-03/HD/NICHD NIH HHS/ -- F32-HD47136/HD/NICHD NIH HHS/ -- GM058231/GM/NIGMS NIH HHS/ -- GM070840/GM/NIGMS NIH HHS/ -- GM61005/GM/NIGMS NIH HHS/ -- GM61464/GM/NIGMS NIH HHS/ -- HD-37105/HD/NICHD NIH HHS/ -- HD039948/HD/NICHD NIH HHS/ -- HD14483/HD/NICHD NIH HHS/ -- HD66219/HD/NICHD NIH HHS/ -- P30-CA14051/CA/NCI NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 ES006272-13/ES/NIEHS NIH HHS/ -- R01 GM070840/GM/NIGMS NIH HHS/ -- R01 HD028152/HD/NICHD NIH HHS/ -- R01ES006272/ES/NIEHS NIH HHS/ -- R37-HD12896/HD/NICHD NIH HHS/ -- RR-15044/RR/NCRR NIH HHS/ -- S19916/Biotechnology and Biological Sciences Research Council/United Kingdom -- T32 GM007601/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):941-52.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095691" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calcification, Physiologic ; Cell Adhesion Molecules/genetics/physiology ; Complement Activation/genetics ; Computational Biology ; Embryonic Development/genetics ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Genes ; *Genome ; Immunity, Innate/genetics ; Immunologic Factors/genetics/physiology ; Male ; Nervous System Physiological Phenomena ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Signal Transduction ; Strongylocentrotus purpuratus/embryology/*genetics/immunology/physiology ; Transcription Factors/genetics
    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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  • 3
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    Unusual biology across a group comprising more than 15% of domain Bacteria (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-06-18
    Description: A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments and are thought to mediate carbon and hydrogen cycles. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing 〉35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise 〉15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50-100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brown, Christopher T -- Hug, Laura A -- Thomas, Brian C -- Sharon, Itai -- Castelle, Cindy J -- Singh, Andrea -- Wilkins, Michael J -- Wrighton, Kelly C -- Williams, Kenneth H -- Banfield, Jillian F -- England -- Nature. 2015 Jul 9;523(7559):208-11. doi: 10.1038/nature14486. Epub 2015 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA. ; Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA. ; 1] School of Earth Sciences, The Ohio State University, Columbus, Ohio 43210, USA [2] Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA. ; Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA. ; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; 1] Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA [2] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [3] Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083755" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*genetics ; *Environmental Microbiology ; Genome, Bacterial/*genetics ; Introns/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ribosomal Proteins/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Identification of long non-coding RNA in the horse transcriptome (2017)
    BioMed Central
    Details
    Publication Date: 2017-07-06
    Description: Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet ...
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 5
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    Tissue resolved, gene structure refined equine transcriptome (2017)
    BioMed Central
    Details
    Publication Date: 2017-01-22
    Description: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the ho...
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 6
    Electronic Resource
    Electronic Resource
    Rapid Centrifugal Estimation of Small Amounts of Sodium (1934)
    s.l. : American Chemical Society
    Industrial and engineering chemistry 6 (1934), S. 202-205 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ac50089a018
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  • 7
    Electronic Resource
    Electronic Resource
    Electrical Conductance of the LiCl–KCl Eutectic Melt Containing Halides and Alkali Titanium Fluorides as Solutes (1958)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 62 (1958), S. 1479-1482 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j150570a003
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  • 8
    Electronic Resource
    Electronic Resource
    Cryoscopy of the LiCl–KCl Eutectic Melt Containing Alkali Halides and Alkali Titanium Fluorides as Solutes (1958)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 62 (1958), S. 823-826 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j150565a013
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  • 9
    Electronic Resource
    Electronic Resource
    A diode-pumped, high gain, planar waveguide, Nd:Y3Al5O12 amplifier (1997)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 71 (1997), S. 876-878 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We report the use of a 5-mm-long planar Nd:yttrium aluminum garnet waveguide grown by liquid-phase epitaxy as an amplifier at 1.064 μm. In a double-pass configuration pumped by a 1.2 W diode laser, small signal gains of 686 (28 dB) have been observed and efficient power extraction demonstrated with output powers of up to 290 mW being obtained. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.119675
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  • 10
    Electronic Resource
    Electronic Resource
    Thermally bonded planar waveguide lasers (1997)
    Woodbury, NY : American Institute of Physics (AIP)
    Applied Physics Letters 71 (1997), S. 1139-1141 
    Details
    ISSN: 1077-3118
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A new technique for fabricating active planar waveguide devices is reported. This process, based on the thermal bonding of precision finished crystal or glass components, allows waveguides to be assembled from very dissimilar materials and could be applied to a wide range of solid state laser or other optical media. The waveguide propagation losses, inferred from the laser performance, are found to be 0.7 dB/cm for Nd:Y3Al5O12 bonded to Y3Al5O12, Nd:Y3Al5O12 bonded to glass, and 0.4 dB/cm for Nd:Gd3Ga5O12 bonded to Y3Al5O12 devices. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.119846
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