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  • 1
    Publication Date: 2010-11-26
    Description: Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3760481/" 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/PMC3760481/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Denoeud, France -- Henriet, Simon -- Mungpakdee, Sutada -- Aury, Jean-Marc -- Da Silva, Corinne -- Brinkmann, Henner -- Mikhaleva, Jana -- Olsen, Lisbeth Charlotte -- Jubin, Claire -- Canestro, Cristian -- Bouquet, Jean-Marie -- Danks, Gemma -- Poulain, Julie -- Campsteijn, Coen -- Adamski, Marcin -- Cross, Ismael -- Yadetie, Fekadu -- Muffato, Matthieu -- Louis, Alexandra -- Butcher, Stephen -- Tsagkogeorga, Georgia -- Konrad, Anke -- Singh, Sarabdeep -- Jensen, Marit Flo -- Huynh Cong, Evelyne -- Eikeseth-Otteraa, Helen -- Noel, Benjamin -- Anthouard, Veronique -- Porcel, Betina M -- Kachouri-Lafond, Rym -- Nishino, Atsuo -- Ugolini, Matteo -- Chourrout, Pascal -- Nishida, Hiroki -- Aasland, Rein -- Huzurbazar, Snehalata -- Westhof, Eric -- Delsuc, Frederic -- Lehrach, Hans -- Reinhardt, Richard -- Weissenbach, Jean -- Roy, Scott W -- Artiguenave, Francois -- Postlethwait, John H -- Manak, J Robert -- Thompson, Eric M -- Jaillon, Olivier -- Du Pasquier, Louis -- Boudinot, Pierre -- Liberles, David A -- Volff, Jean-Nicolas -- Philippe, Herve -- Lenhard, Boris -- Roest Crollius, Hugues -- Wincker, Patrick -- Chourrout, Daniel -- Z01 LM000073-12/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Dec 3;330(6009):1381-5. doi: 10.1126/science.1194167. Epub 2010 Nov 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Commissariat a l'Energie Atomique, Institut de Genomique, Genoscope, Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097902" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; DNA Transposable Elements ; DNA, Intergenic ; Exons ; Gene Order ; Genes, Duplicate ; Genes, Homeobox ; *Genome ; Introns ; Invertebrates/classification/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Spliceosomes/metabolism ; Synteny ; Urochordata/anatomy & histology/classification/*genetics/immunology ; Vertebrates/classification/genetics
    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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  • 2
    Publication Date: 2011-10-25
    Description: The tip of a projectile point made of mastodon bone is embedded in a rib of a single disarticulated mastodon at the Manis site in the state of Washington. Radiocarbon dating and DNA analysis show that the rib is associated with the other remains and dates to 13,800 years ago. Thus, osseous projectile points, common to the Beringian Upper Paleolithic and Clovis, were made and used during pre-Clovis times in North America. The Manis site, combined with evidence of mammoth hunting at sites in Wisconsin, provides evidence that people were hunting proboscideans at least two millennia before Clovis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Waters, Michael R -- Stafford, Thomas W Jr -- McDonald, H Gregory -- Gustafson, Carl -- Rasmussen, Morten -- Cappellini, Enrico -- Olsen, Jesper V -- Szklarczyk, Damian -- Jensen, Lars Juhl -- Gilbert, M Thomas P -- Willerslev, Eske -- New York, N.Y. -- Science. 2011 Oct 21;334(6054):351-3. doi: 10.1126/science.1207663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Study of the First Americans, Department of Anthropology, Texas A&M University, 4352 TAMU, College Station, TX 77843-4352, USA. mwaters@tamu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22021854" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Archaeology ; Bone and Bones ; Geologic Sediments ; History, Ancient ; Humans ; Male ; *Mastodons ; Radiometric Dating ; Time ; Washington ; Weapons/*history
    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
    Publication Date: 2014-05-31
    Description: The most prominent pattern in global marine biogeography is the biodiversity peak in the Indo-Australian Archipelago. Yet the processes that underpin this pattern are still actively debated. By reconstructing global marine paleoenvironments over the past 3 million years on the basis of sediment cores, we assessed the extent to which Quaternary climate fluctuations can explain global variation in current reef fish richness. Comparing global historical coral reef habitat availability with the present-day distribution of 6316 reef fish species, we find that distance from stable coral reef habitats during historical periods of habitat loss explains 62% of the variation in fish richness, outweighing present-day environmental factors. Our results highlight the importance of habitat persistence during periods of climate change for preserving marine biodiversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pellissier, Loic -- Leprieur, Fabien -- Parravicini, Valeriano -- Cowman, Peter F -- Kulbicki, Michel -- Litsios, Glenn -- Olsen, Steffen M -- Wisz, Mary S -- Bellwood, David R -- Mouillot, David -- New York, N.Y. -- Science. 2014 May 30;344(6187):1016-9. doi: 10.1126/science.1249853.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Fribourg, Department of Biology, Chemin du Musee 10, CH-1700 Fribourg, Switzerland. Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. CESAB (Centre de Synthese et d'Analyse sur la Biodiversite)-FRB (Fondation pour la Recherche sur la Biodiversite), Immeuble Henri Poincare, Domaine du Petit Arbois, FR-13857 Aix-en-Provence cedex 3, France. ; Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia. ; IRD, UR 227 CoReUs, LABEX (Laboratoire d'Excellence) Corail, Laboratoire Arago, Boite Postale 44, FR-66651 Banyuls/mer, France. ; Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland. Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland. ; Center for Ocean and Ice, Danish Meteorological Institute, Lyngbyvej 100, 2100 Copenhagen, Denmark. ; Department of Bioscience, Aarhus University, 8000 C Aarhus, Denmark. Department of Ecology and Environment, DHI Water and Environment, 2970 Horsholm, Denmark. ; Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. ; Laboratoire Ecologie des Systemes Marins Cotiers UMR 5119, CNRS, Institut de Recherche pour le Developpement (IRD), Institut Francais de Recherche pour l'Exploitation de la Mer, UM2, UM1, cc 093, Place E. Bataillon, FR-34095 Montpellier Cedex 5, France. Australian Research Council Centre of Excellence for Coral Reef Studies, and School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia. david.mouillot@univ-montp2.fr.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24876495" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Australia ; *Biodiversity ; *Climate Change ; *Conservation of Natural Resources ; *Coral Reefs ; *Fishes
    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
    Publication Date: 2012-08-07
    Description: In plants, transport processes are important for the reallocation of defence compounds to protect tissues of high value, as demonstrated in the plant model Arabidopsis, in which the major defence compounds, glucosinolates, are translocated to seeds on maturation. The molecular basis for long-distance transport of glucosinolates and other defence compounds, however, remains unknown. Here we identify and characterize two members of the nitrate/peptide transporter family, GTR1 and GTR2, as high-affinity, proton-dependent glucosinolate-specific transporters. The gtr1 gtr2 double mutant did not accumulate glucosinolates in seeds and had more than tenfold over-accumulation in source tissues such as leaves and silique walls, indicating that both plasma membrane-localized transporters are essential for long-distance transport of glucosinolates. We propose that GTR1 and GTR2 control the loading of glucosinolates from the apoplasm into the phloem. Identification of the glucosinolate transporters has agricultural potential as a means to control allocation of defence compounds in a tissue-specific manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nour-Eldin, Hussam Hassan -- Andersen, Tonni Grube -- Burow, Meike -- Madsen, Svend Roesen -- Jorgensen, Morten Egevang -- Olsen, Carl Erik -- Dreyer, Ingo -- Hedrich, Rainer -- Geiger, Dietmar -- Halkier, Barbara Ann -- England -- Nature. 2012 Aug 23;488(7412):531-4. doi: 10.1038/nature11285.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871Frederiksberg C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22864417" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arabidopsis/embryology/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Biological Transport/drug effects ; Cell Extracts/chemistry ; Evolution, Molecular ; Gene Deletion ; Gene Library ; Genes, Plant/genetics ; Glucosinolates/*metabolism/pharmacology ; Monosaccharide Transport Proteins/deficiency/genetics/*metabolism ; Oocytes/drug effects/metabolism ; Organ Specificity ; Phloem/metabolism ; Protons ; Seeds/*metabolism ; Xenopus laevis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2012-03-01
    Description: After entering the cerebral cortex, sensory information spreads through six different horizontal neuronal layers that are interconnected by vertical axonal projections. It is believed that through these projections layers can influence each other's response to sensory stimuli, but the specific role that each layer has in cortical processing is still poorly understood. Here we show that layer six in the primary visual cortex of the mouse has a crucial role in controlling the gain of visually evoked activity in neurons of the upper layers without changing their tuning to orientation. This gain modulation results from the coordinated action of layer six intracortical projections to superficial layers and deep projections to the thalamus, with a substantial role of the intracortical circuit. This study establishes layer six as a major mediator of cortical gain modulation and suggests that it could be a node through which convergent inputs from several brain areas can regulate the earliest steps of cortical visual processing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636977/" 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/PMC3636977/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Shawn R -- Bortone, Dante S -- Adesnik, Hillel -- Scanziani, Massimo -- 5T32NS007220-28/NS/NINDS NIH HHS/ -- R01 NS069010/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Feb 22;483(7387):47-52. doi: 10.1038/nature10835.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Center for Neural Circuits and Behavior, Neurobiology Section and Department of Neuroscience, University of California San Diego, La Jolla, California 92093-0634, USA. srolsen@ucsd.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22367547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Mice ; Models, Neurological ; Neural Inhibition/radiation effects ; Neural Pathways/*physiology/radiation effects ; Neurons/physiology/radiation effects ; Photic Stimulation ; Synapses/metabolism/radiation effects ; Thalamic Nuclei/cytology/physiology/radiation effects ; Visual Cortex/anatomy & histology/*cytology/*physiology/radiation effects ; Visual Perception/*physiology/radiation effects
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2013-06-28
    Description: The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Orlando, Ludovic -- Ginolhac, Aurelien -- Zhang, Guojie -- Froese, Duane -- Albrechtsen, Anders -- Stiller, Mathias -- Schubert, Mikkel -- Cappellini, Enrico -- Petersen, Bent -- Moltke, Ida -- Johnson, Philip L F -- Fumagalli, Matteo -- Vilstrup, Julia T -- Raghavan, Maanasa -- Korneliussen, Thorfinn -- Malaspinas, Anna-Sapfo -- Vogt, Josef -- Szklarczyk, Damian -- Kelstrup, Christian D -- Vinther, Jakob -- Dolocan, Andrei -- Stenderup, Jesper -- Velazquez, Amhed M V -- Cahill, James -- Rasmussen, Morten -- Wang, Xiaoli -- Min, Jiumeng -- Zazula, Grant D -- Seguin-Orlando, Andaine -- Mortensen, Cecilie -- Magnussen, Kim -- Thompson, John F -- Weinstock, Jacobo -- Gregersen, Kristian -- Roed, Knut H -- Eisenmann, Vera -- Rubin, Carl J -- Miller, Donald C -- Antczak, Douglas F -- Bertelsen, Mads F -- Brunak, Soren -- Al-Rasheid, Khaled A S -- Ryder, Oliver -- Andersson, Leif -- Mundy, John -- Krogh, Anders -- Gilbert, M Thomas P -- Kjaer, Kurt -- Sicheritz-Ponten, Thomas -- Jensen, Lars Juhl -- Olsen, Jesper V -- Hofreiter, Michael -- Nielsen, Rasmus -- Shapiro, Beth -- Wang, Jun -- Willerslev, Eske -- RC2 HG005598/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Jul 4;499(7456):74-8. doi: 10.1038/nature12323. Epub 2013 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen K, Denmark. Lorlando@snm.ku.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23803765" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Conservation of Natural Resources ; DNA/analysis/genetics ; Endangered Species ; Equidae/classification/genetics ; *Evolution, Molecular ; Fossils ; Genetic Variation/genetics ; Genome/*genetics ; History, Ancient ; Horses/classification/*genetics ; *Phylogeny ; Proteins/analysis/chemistry/genetics ; Yukon Territory
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2014-09-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Bjorn R -- England -- Nature. 2014 Sep 25;513(7519):494-5. doi: 10.1038/nature13750. Epub 2014 Sep 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25231860" target="_blank"〉PubMed〈/a〉
    Keywords: Achondroplasia/*drug therapy/*pathology ; Animals ; Female ; Hydroxymethylglutaryl-CoA Reductase Inhibitors/*therapeutic use ; Male ; Receptor, Fibroblast Growth Factor, Type 3/*deficiency/*genetics ; Thanatophoric Dysplasia/*drug therapy/*pathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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