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  • 1
    Publication Date: 1987-07-03
    Description: The distribution of cells containing messenger RNA that encodes amyloid beta protein was determined in hippocampi and in various cortical regions from cynomolgus monkeys, normal humans, and patients with Alzheimer's disease by in situ hybridization. Both 35S-labeled RNA antisense and sense probes to amyloid beta protein messenger RNA were used to ensure specific hybridization. Messenger RNA for amyloid beta protein was expressed in a subset of neurons in the prefrontal cortex from monkeys, normal humans, and patients with Alzheimer's disease. This messenger RNA was also present in the neurons of all the hippocampal fields from monkeys, normal humans and, although to a lesser extent in cornu ammonis 1, patients with Alzheimer's disease. The distribution of amyloid beta protein messenger RNA was similar to that of the neurofibrillary tangles of Alzheimer's disease in some regions, but the messenger RNA was also expressed in other neurons that are not usually involved in the pathology of Alzheimer's disease.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bahmanyar, S -- Higgins, G A -- Goldgaber, D -- Lewis, D A -- Morrison, J H -- Wilson, M C -- Shankar, S K -- Gajdusek, D C -- AG05131/AG/NIA NIH HHS/ -- MH00519/MH/NIMH NIH HHS/ -- NS23038/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1987 Jul 3;237(4810):77-80.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3299701" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/*genetics ; Amyloid/*genetics ; Amyloid beta-Peptides ; Animals ; Brain/*physiopathology ; Cerebral Cortex/physiology ; Gene Expression Regulation ; Hippocampus/physiology ; Humans ; Macaca fascicularis ; Nucleic Acid Hybridization ; RNA, Messenger/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: 2014-01-31
    Description: Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such 'talented' producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus 'Entotheonella' with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. 'Entotheonella' spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum 'Tectomicrobia'. The pronounced bioactivities and chemical uniqueness of 'Entotheonella' compounds provide significant opportunities for ecological studies and drug discovery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wilson, Micheal C -- Mori, Tetsushi -- Ruckert, Christian -- Uria, Agustinus R -- Helf, Maximilian J -- Takada, Kentaro -- Gernert, Christine -- Steffens, Ursula A E -- Heycke, Nina -- Schmitt, Susanne -- Rinke, Christian -- Helfrich, Eric J N -- Brachmann, Alexander O -- Gurgui, Cristian -- Wakimoto, Toshiyuki -- Kracht, Matthias -- Crusemann, Max -- Hentschel, Ute -- Abe, Ikuro -- Matsunaga, Shigeki -- Kalinowski, Jorn -- Takeyama, Haruko -- Piel, Jorn -- England -- Nature. 2014 Feb 6;506(7486):58-62. doi: 10.1038/nature12959. Epub 2014 Jan 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Institute of Microbiology, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland [2] Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany [3]. ; 1] Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan [2]. ; Institute for Genome Research and Systems Biology, Center for Biotechnology, Universitat Bielefeld, Universitatstrasse 25, 33594 Bielefeld, Germany. ; 1] Institute of Microbiology, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland [2] Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany. ; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. ; Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wurzburg, Julius-von-Sachs-Platz 3, 97082 Wurzburg, Germany. ; Kekule Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany. ; Department of Earth and Environmental Sciences, Palaeontology and Geobiology, Ludwig Maximilians University Munich, Richard-Wagner-Strasse 10, 80333 Munich, Germany. ; Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA. ; Institute of Microbiology, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland. ; Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. ; Faculty of Science and Engineering, Waseda University Center for Advanced Biomedical Sciences, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24476823" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biosynthetic Pathways/genetics ; Deltaproteobacteria/*classification/genetics/*metabolism/physiology ; *Drug Discovery ; Environmental Microbiology ; Genes, Bacterial/genetics ; Genome, Bacterial/genetics ; Metagenomics ; Molecular Sequence Data ; Multigene Family/genetics ; Peptides/metabolism ; Polyketides/metabolism ; Porifera/metabolism/microbiology ; Single-Cell Analysis ; Symbiosis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2004-11-30
    Description: The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, Beth -- Drummond, Alexei J -- Rambaut, Andrew -- Wilson, Michael C -- Matheus, Paul E -- Sher, Andrei V -- Pybus, Oliver G -- Gilbert, M Thomas P -- Barnes, Ian -- Binladen, Jonas -- Willerslev, Eske -- Hansen, Anders J -- Baryshnikov, Gennady F -- Burns, James A -- Davydov, Sergei -- Driver, Jonathan C -- Froese, Duane G -- Harington, C Richard -- Keddie, Grant -- Kosintsev, Pavel -- Kunz, Michael L -- Martin, Larry D -- Stephenson, Robert O -- Storer, John -- Tedford, Richard -- Zimov, Sergei -- Cooper, Alan -- New York, N.Y. -- Science. 2004 Nov 26;306(5701):1561-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15567864" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Animals ; Bayes Theorem ; *Bison/classification/genetics ; Canada ; China ; *Climate ; DNA, Mitochondrial/genetics ; Environment ; *Fossils ; Genetic Variation ; Genetics, Population ; Human Activities ; Humans ; North America ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Time
    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: 1996-06-14
    Description: Analyses of fossil mammal faunas from 2945 localities in the United States demonstrate that the geographic ranges of individual species shifted at different times, in different directions, and at different rates in response to late Quaternary environmental fluctuations. The geographic pattern of faunal provinces was similar for the late Pleistocene and late Holocene, but differing environmental gradients resulted in dissimilar species composition for these biogeographic regions. Modern community patterns emerged only in the last few thousand years, and many late Pleistocene communities do not have modern analogs. Faunal heterogeneity was greater in the late Pleistocene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graham -- Lundelius Jr -- Schroeder -- Toomey III -- Anderson -- Barnosky -- Burns -- Churcher -- Grayson -- Guthrie -- Harington -- Jefferson -- Martin -- McDonald -- Morlan -- Semken Jr -- Webb -- Werdelin -- Wilson -- New York, N.Y. -- Science. 1996 Jun 14;272(5268):1601-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉R. W. Graham, M. A. Graham, E. K. Schroeder, and R. S. Toomey III are at Research and Collections Center, Illinois State Museum, 1011 East Ash, Springfield, IL 62703, USA. E. L. Lundelius Jr., Department of Geological Sciences, University of Texas, Austin, TX 78712, USA. E. Anderson, Denver Museum of Natural History, Denver, CO 80205, USA. A. D. Barnosky, Mountain Research Center, Montana State University, Bozeman, MT 59715, USA. J. A. Burns, Provincial Museum of Alberta, Edmonton, Alberta, Canada T5N 0M6. C. S. Churcher, Department of Zoology, University of Toronto, Toronto, Ontario, Canada M5S 1A1. D. K. Grayson, Department of Anthropology, University of Washington, Seattle, WA 98195, USA. R. D. Guthrie, Department of Biology, University of Alaska, Fairbanks, AK 99701, USA. C. R. Harington, Earth Sciences Section (Paleobiology), Canadian Museum of Nature, Ottawa, Ontario, Canada K1P 6P4. G. T. Jefferson, Anza-Borrego Desert State Park, 200 Palm Canyon Drive, Borrego Springs, CA 92004, USA. L. D. Martin, Museum of Natural History, University of Kansas, Lawrence, KS 66045, USA. H. G. McDonald, Hagerman Fossil Beds National Monument, Post Office Box 570, Hagerman, ID 83332, USA. R. E. Morlan, Canadian Museum of Civilization, Post Office Box 3100 Station B, Hull, Quebec, Canada J8X 4H2. H. A. Semken Jr., Department of Geology, University of Iowa, Iowa City, IA 52242, USA. S. D. Webb, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. L. Werdelin, Department of Paleozoology, Swedish Museum, Box 50007, S-104 05 Stockholm, Sweden. M. C. Wilson, Department of Archaeology, Simon Fraser University, Burnaby, BC, Canada V5A 1S6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662471" target="_blank"〉PubMed〈/a〉
    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
    Publication Date: 2018-06-08
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  • 6
    Publication Date: 2018-06-08
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  • 7
    Publication Date: 2019-02-01
    Description: Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium.
    Type: Article , PeerReviewed
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    Format: other
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  • 8
    Publication Date: 2017-06-26
    Description: Information-theoretic concepts in theory of random graphs - entropy functions for probability distributions and Markov chains
    Keywords: MATHEMATICS
    Type: NASA-CR-478
    Format: application/pdf
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  • 9
    Publication Date: 2016-12-19
    Description: Marine sponges are a rich source of bioactive natural products and are promising sources for drug discovery and development An impressive example is the sponge Theonella swinhoei, which has yielded more than 120 compounds belonging to diverse structural types. Many sponges also harbor highly complex consortia of symbiotic bacteria that are suspected to be the true source of at least some of the secondary metabolites. In previous work, our group demonstrated a bacterial origin of onnamide- and psymberin-type polyketides for two different sponges (1–3), but there were no insights into the producer of compounds from other natural product families. In addition, the exact taxonomic identity of sponge-associated producers remained unknown. This talk will present new insights into these two issues. Isolation of genes encoding a peptide biosynthetic pathway from the T. swinhoei metagenome demonstrated a bacterial origin. Several genes were heterologously expressed and functionally characterized, which revealed unprecedented biosynthetic transformations. The novelty of these modifications suggests the existence of a structurally distinct natural product family, for which we propose the name proteusins. Using a strategy consisting of single-cell analysis and metagenomic sequencing, we identified the bacterial producer of onnamide polyketides in T. swinhoei. Surprisingly, the data suggest the symbiont to be a chemically exceptionally prolific bacterium, producing not only onnamides but most other compounds from this sponge chemotype, including the known and two previously unknown proteusins. Further biosynthetic studies and a survey of other sponges indicate that close relatives of the producer are widespread in these animals and vary with respect to their biosynthetic capabilities. These bacteria might therefore represent the first uncultivated taxon with a metabolic richness resembling that of major cultivated bacterial natural product sources. These results reveal a key role of symbiotic bacteria in the chemistry of their sponge hosts and provide new strategies to study uncultivated symbionts in a more systematic fashion.
    Type: Article , PeerReviewed
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  • 10
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