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  • 1
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    Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Acoelomorph flatworms are deuterostomes related to Xenoturbella (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-02-11
    Description: Xenoturbellida and Acoelomorpha are marine worms with contentious ancestry. Both were originally associated with the flatworms (Platyhelminthes), but molecular data have revised their phylogenetic positions, generally linking Xenoturbellida to the deuterostomes and positioning the Acoelomorpha as the most basally branching bilaterian group(s). Recent phylogenomic data suggested that Xenoturbellida and Acoelomorpha are sister taxa and together constitute an early branch of Bilateria. Here we assemble three independent data sets-mitochondrial genes, a phylogenomic data set of 38,330 amino-acid positions and new microRNA (miRNA) complements-and show that the position of Acoelomorpha is strongly affected by a long-branch attraction (LBA) artefact. When we minimize LBA we find consistent support for a position of both acoelomorphs and Xenoturbella within the deuterostomes. The most likely phylogeny links Xenoturbella and Acoelomorpha in a clade we call Xenacoelomorpha. The Xenacoelomorpha is the sister group of the Ambulacraria (hemichordates and echinoderms). We show that analyses of miRNA complements have been affected by character loss in the acoels and that both groups possess one miRNA and the gene Rsb66 otherwise specific to deuterostomes. In addition, Xenoturbella shares one miRNA with the ambulacrarians, and two with the acoels. This phylogeny makes sense of the shared characteristics of Xenoturbellida and Acoelomorpha, such as ciliary ultrastructure and diffuse nervous system, and implies the loss of various deuterostome characters in the Xenacoelomorpha including coelomic cavities, through gut and gill slits.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025995/" 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/PMC4025995/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Philippe, Herve -- Brinkmann, Henner -- Copley, Richard R -- Moroz, Leonid L -- Nakano, Hiroaki -- Poustka, Albert J -- Wallberg, Andreas -- Peterson, Kevin J -- Telford, Maximilian J -- 075491/Z/04/Wellcome Trust/United Kingdom -- R01 NS039103/NS/NINDS NIH HHS/ -- R21 DA030118/DA/NIDA NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Feb 10;470(7333):255-8. doi: 10.1038/nature09676.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre Robert-Cedergren, Departement de Biochimie, Universite de Montreal, Succursale Centre-Ville, Montreal, Quebec H3C 3J7, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21307940" target="_blank"〉PubMed〈/a〉
    Keywords: Anal Canal ; Animals ; Aquatic Organisms/*classification/genetics/physiology ; Bayes Theorem ; Expressed Sequence Tags ; Gills ; MicroRNAs/genetics ; Mitochondrial Proteins/genetics ; *Phylogeny
    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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  • 3
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    The African coelacanth genome provides insights into tetrapod evolution (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-04-20
    Description: The discovery of a living coelacanth specimen in 1938 was remarkable, as this lineage of lobe-finned fish was thought to have become extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features. Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633110/" 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/PMC3633110/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Amemiya, Chris T -- Alfoldi, Jessica -- Lee, Alison P -- Fan, Shaohua -- Philippe, Herve -- Maccallum, Iain -- Braasch, Ingo -- Manousaki, Tereza -- Schneider, Igor -- Rohner, Nicolas -- Organ, Chris -- Chalopin, Domitille -- Smith, Jeramiah J -- Robinson, Mark -- Dorrington, Rosemary A -- Gerdol, Marco -- Aken, Bronwen -- Biscotti, Maria Assunta -- Barucca, Marco -- Baurain, Denis -- Berlin, Aaron M -- Blatch, Gregory L -- Buonocore, Francesco -- Burmester, Thorsten -- Campbell, Michael S -- Canapa, Adriana -- Cannon, John P -- Christoffels, Alan -- De Moro, Gianluca -- Edkins, Adrienne L -- Fan, Lin -- Fausto, Anna Maria -- Feiner, Nathalie -- Forconi, Mariko -- Gamieldien, Junaid -- Gnerre, Sante -- Gnirke, Andreas -- Goldstone, Jared V -- Haerty, Wilfried -- Hahn, Mark E -- Hesse, Uljana -- Hoffmann, Steve -- Johnson, Jeremy -- Karchner, Sibel I -- Kuraku, Shigehiro -- Lara, Marcia -- Levin, Joshua Z -- Litman, Gary W -- Mauceli, Evan -- Miyake, Tsutomu -- Mueller, M Gail -- Nelson, David R -- Nitsche, Anne -- Olmo, Ettore -- Ota, Tatsuya -- Pallavicini, Alberto -- Panji, Sumir -- Picone, Barbara -- Ponting, Chris P -- Prohaska, Sonja J -- Przybylski, Dariusz -- Saha, Nil Ratan -- Ravi, Vydianathan -- Ribeiro, Filipe J -- Sauka-Spengler, Tatjana -- Scapigliati, Giuseppe -- Searle, Stephen M J -- Sharpe, Ted -- Simakov, Oleg -- Stadler, Peter F -- Stegeman, John J -- Sumiyama, Kenta -- Tabbaa, Diana -- Tafer, Hakim -- Turner-Maier, Jason -- van Heusden, Peter -- White, Simon -- Williams, Louise -- Yandell, Mark -- Brinkmann, Henner -- Volff, Jean-Nicolas -- Tabin, Clifford J -- Shubin, Neil -- Schartl, Manfred -- Jaffe, David B -- Postlethwait, John H -- Venkatesh, Byrappa -- Di Palma, Federica -- Lander, Eric S -- Meyer, Axel -- Lindblad-Toh, Kerstin -- 095908/Wellcome Trust/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- P42 ES007381/ES/NIEHS NIH HHS/ -- R01 ES006272/ES/NIEHS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 OD011116/OD/NIH HHS/ -- R24 OD011199/OD/NIH HHS/ -- R24 RR032670/RR/NCRR NIH HHS/ -- R37 HD032443/HD/NICHD NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA. camemiya@benaroyaresearch.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23598338" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified ; *Biological Evolution ; Chick Embryo ; Conserved Sequence/genetics ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; Extremities/anatomy & histology/growth & development ; Fishes/anatomy & histology/*classification/*genetics/physiology ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Immunoglobulin M/genetics ; Mice ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Vertebrates/anatomy & histology/genetics/physiology
    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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    The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: single-probe measurements and the strong power of f(z){sigma}8(z) on constraining dark energy (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-26
    Description: We present measurements of the anisotropic galaxy clustering from the Data Release 9 (DR9) CMASS sample of the Sloan Digital Sky Survey (SDSS)-III Baryon Oscillation Spectroscopic Survey (BOSS). We analyse the broad-range shape of the monopole and quadrupole correlation functions to obtain constraints, at the effective redshift z  = 0.57 of the sample, on the Hubble expansion rate H ( z ), the angular-diameter distance D A ( z ), the normalized growth rate f ( z ) 8 ( z ), the physical matter density m h 2 , and the biased amplitude of matter fluctuation b 8 ( z ). We obtain { H (0.57), D A (0.57), f (0.57) 8 (0.57), m h 2 , b 8 (0.57)} = $\lbrace 87.6_{-6.8}^{+6.7}$ kms –1 Mpc –1 , 1396 ± 73 Mpc, 0.428 ± 0.066, $0.126_{-0.010}^{+0.008}$ , 1.19 ± 0.14} and their covariance matrix as well. The parameters which are not well constrained by our galaxy clustering analysis are marginalized over with wide flat priors. Since no priors from other data sets [i.e. cosmic microwave background (CMB)] are adopted and no dark energy models are assumed, our results from BOSS CMASS galaxy clustering alone may be combined with other data sets, i.e. CMB, SNe, lensing or other galaxy clustering data to constrain the parameters of a given cosmological model. We show that the major power on constraining dark energy from the anisotropic galaxy clustering signal, as compared to the angular-averaged one (monopole), arises from including the normalized growth rate f ( z ) 8 ( z ). In the case of the cosmological model assuming a constant dark energy equation of state and a flat universe ( w CDM), our single-probe CMASS constraints, combined with CMB ( WMAP 9+SPT), yield a value for the dark energy equation-of-state parameter of w  = –0.90 ± 0.11. Therefore, it is important to include f ( z ) 8 ( z ) while investigating the nature of dark energy with current and upcoming large-scale galaxy surveys.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
    Electronic Resource
    Electronic Resource
    Riemann spaces conformal to Einstein spaces (1924)
    Springer
    Mathematische Annalen 91 (1924), S. 269-278 
    Details
    ISSN: 1432-1807
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01556083
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  • 6
    Electronic Resource
    Electronic Resource
    Einstein spaces which are mapped conformally on each other (1925)
    Springer
    Mathematische Annalen 94 (1925), S. 119-145 
    Details
    ISSN: 1432-1807
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01208647
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  • 7
    Electronic Resource
    Electronic Resource
    1.3-dioxolan-4-on-2-ylium- und 1.3-dioxan-4-on-2-ylium hexachloroantimonate, neue typen cyclischer oxoniumsalze.
    Amsterdam : Elsevier
    Tetrahedron Letters 13 (1972), S. 5221-5224 
    Details
    ISSN: 0040-4039
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/S0040-4039(01)85213-8
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  • 8
    Electronic Resource
    Electronic Resource
    Ein Selektionsmodell für das Rhesus-Blutgruppensystem (1973)
    Springer
    Human genetics 〈Berlin〉 19 (1973), S. 111-122 
    Details
    ISSN: 1432-1203
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Description / Table of Contents: Zusammenfassung Es wird ein Selektionsmodell für das Rhesus-Blutgruppensystem aufgestellt, das die Berechnung von Selektionskoeffizienten in den beiden betroffenen Paarungstypen unter Berücksichtigung der Rangzahl der immunisierenden Schwangerschaft und der Kinderzahl in kompletten Familien einer Bevölkerung erlaubt. Die Anwendung auf menschliche Bevölkerungen zeigt die Abhängigkeit des Selektionskoeffizienten von der Bevölkerungsstruktur. Rb symbol for genes determining the property “Rhesus positive” rh symbol for genes determining the property “Rhesus negative” a i frequency of immunization of rhrh women by the i-th pregnancy with an Rhrh fetus fb frequency of complete families with b offspring in a population p frequency of Rh genes in a population q frequency of rh genes in a population s 1 selection coefficient for Rhrh offspring due to selection in matings of the type wife (F) rhrh/husband (M) RhRh (Mating type 1) s 2 selection coefficient for Rhrh offspring due to selection in matings of the type Frhrh/MRhrh (mating type 2) s=s 1+s 2 total Rhesus selection coefficient Z b,i number of Rhrh offspring undergoing selection in matings of type 2 with a total number of b offspring and with immunization of the mother by the i-th pregnancy. All combinations of Rhrh and rhrh children possible with given values of b and i have to be considered. Figs. 1 and 2 demonstrate Z b,i graphically for b=(1),2,3,4 and i=1,2.
    Notes: Summary Natural selection in the Rhesus blood-group system is characterized by a disadvantage of the heterozygotes. According to Haldane (1942) a biallelic system with selection against the heterozygote is unstable with a tendency of eliminating the rarer allele. Previously reported selection models did not consider several peculiarities of the Rhesus system, e.g. the fact that only a fraction of the Rhesus negative mothers giving birth to Rhesus positive children is immunized, and that selection is directed only against Rhesus positive children of Rhesus negative mothers born after the immunizing pregnancy. For these reasons, population structure, more specifically the number of offspring of reproducing couples in a population, is a determinant of Rhesus selection. the selection model presented here takes these factors into consideration. Application to human populations shows the magnitude of the effects of the above mentioned factors on the selection coefficient. In order to facilitate understanding the formulas and calculations, the definitions described in part 2 are given in English
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00295239
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  • 9
    Electronic Resource
    Electronic Resource
    Färberische Beobachtungen zur Frage nach dem primären Bildungsort von Neurosekret im supraoptico-hypophysären System (1968)
    Springer
    Cell & tissue research 87 (1968), S. 534-544 
    Details
    ISSN: 1432-0878
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Description / Table of Contents: Zusammenfassung An Embryonen und Jungtieren von Maus und Huhn wurde die Entwicklung des neurosekretorischen hypothalamo-hypophysären Systems untersucht. Dabei gelang es, neurosekretorisches Material in den Perikaryen des Systems zum gleichen Zeitpunkt nachzuweisen, zu dem es in der Neurohypophyse erstmalig auftrat. In vergleichend-anatomischen Untersuchungen an erwachsenen Tieren ließ sich bei einer Reihe von Säugetierarten Neurosekret im Verlauf des gesamten Neurons sichtbar machen. Korrespondierende Neuronabschnitte verschiedener Spezies enthielten dabei vergleichbare Neurosekretmengen. Die Befunde wurden mit verbesserten Verfahren zur färberischen Darstellung von Neurosekret gewonnen. Die von ihnen abweichenden Ergebnisse früherer Untersuchungen beruhen auf unzulänglichen Methoden und können daher nicht gegen die Hypothese eines intraaxonalen Neurosekret-Transportes ins Feld geführt werden.
    Notes: Summary The development of the neurosecretory hypothalamo-hypophyseal system of mouse and chick embryos has been studied. Neurosecretory granules could be identified in the perikarya of the neurosecretory cells simultaneously with their first appearance in the neurohypophysis. Subsequently, a variety of adult mammalian species was investigated. In all cases, neurosecretory material could be demonstrated along the whole length of the neurons. Comparison of corresponding parts of the neurons showed them to contain comparable amounts of neurosecretory material. The investigations were carried out with improved techniques for staining neurosecretory material. Results of earlier investigations, inconsistent with these findings, were obtained with inadequate methods and cannot be regarded as contradicting the hypothesis of an intraaxonal transport of neurosecretory material.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00325584
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  • 10
    Electronic Resource
    Electronic Resource
    Gomori-positive elementary granules in inner and outer layer of the infundibulum (1975)
    Springer
    Cell & tissue research 163 (1975), S. 503-508 
    Details
    ISSN: 1432-0878
    Keywords: Infundibulum ; Gomori-positive elementary granules ; Mammals ; Birds ; Fish
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary With the gallocyanine technique (Wittkowski, Bock and Franken, 1970) Gomori-positive substances of the infundibulum can be stained for light- and electron-microscopic examination. In various mammalian species, the size of Gomori-positive elementary granules in the outer layer is markedly different from that in the inner layer of the infundibulum. In general, the granules of the outer layer have less then half the diameter of those of the inner layer. In birds and fish, however, only small differences were found between the granules of both layers. The significance of the results is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00218495
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