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University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
An Integrative Approach Sheds New Light Onto the Systematics
www.nature.com/scientificreports OPEN An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea) Thomas Pröschold1*, Daniel Rieser1, Tatyana Darienko2, Laura Nachbaur1, Barbara Kammerlander1, Kuimei Qian1,3, Gianna Pitsch4, Estelle Patricia Bruni4,5, Zhishuai Qu6, Dominik Forster6, Cecilia Rad‑Menendez7, Thomas Posch4, Thorsten Stoeck6 & Bettina Sonntag1 Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of diferent Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one‑year cycle both from morphospecies counts and high‑ throughput sequencing (HTS), and, (v) proof of the co‑occurrence of Coleps and their endosymbiotic algae from HTS‑based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in diferent depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the diferent lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). -
Plant Life MagillS Encyclopedia of Science
MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE MAGILLS ENCYCLOPEDIA OF SCIENCE PLANT LIFE Volume 4 Sustainable Forestry–Zygomycetes Indexes Editor Bryan D. Ness, Ph.D. Pacific Union College, Department of Biology Project Editor Christina J. Moose Salem Press, Inc. Pasadena, California Hackensack, New Jersey Editor in Chief: Dawn P. Dawson Managing Editor: Christina J. Moose Photograph Editor: Philip Bader Manuscript Editor: Elizabeth Ferry Slocum Production Editor: Joyce I. Buchea Assistant Editor: Andrea E. Miller Page Design and Graphics: James Hutson Research Supervisor: Jeffry Jensen Layout: William Zimmerman Acquisitions Editor: Mark Rehn Illustrator: Kimberly L. Dawson Kurnizki Copyright © 2003, by Salem Press, Inc. All rights in this book are reserved. No part of this work may be used or reproduced in any manner what- soever or transmitted in any form or by any means, electronic or mechanical, including photocopy,recording, or any information storage and retrieval system, without written permission from the copyright owner except in the case of brief quotations embodied in critical articles and reviews. For information address the publisher, Salem Press, Inc., P.O. Box 50062, Pasadena, California 91115. Some of the updated and revised essays in this work originally appeared in Magill’s Survey of Science: Life Science (1991), Magill’s Survey of Science: Life Science, Supplement (1998), Natural Resources (1998), Encyclopedia of Genetics (1999), Encyclopedia of Environmental Issues (2000), World Geography (2001), and Earth Science (2001). ∞ The paper used in these volumes conforms to the American National Standard for Permanence of Paper for Printed Library Materials, Z39.48-1992 (R1997). Library of Congress Cataloging-in-Publication Data Magill’s encyclopedia of science : plant life / edited by Bryan D. -
Evaluating the Congruence Between DNA‐Based and Morphological
Limnol. Oceanogr. 9999, 2021, 1–20 © 2021 The Authors. Limnology and Oceanography published by Wiley Periodicals LLC on behalf of Association for the Sciences of Limnology and Oceanography. doi: 10.1002/lno.11856 Evaluating the congruence between DNA-based and morphological taxonomic approaches in water and sediment trap samples: Analyses of a 36-month time series from a temperate monomictic lake Joanna Gauthier ,1,2* David Walsh ,2,3 Daniel T. Selbie,4 Alyssa Bourgeois,1 Katherine Griffiths,1,2 Isabelle Domaizon,4,5 Irene Gregory-Eaves1,2 1Department of Biology, McGill University, Montreal, Quebec, Canada 2Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montreal, Quebec, Canada 3Department of Biology, Concordia University, Montreal, Quebec, Canada 4Fisheries and Oceans Canada, Pacific Region, Science Branch, Ecosystem Sciences Division, Cultus Lake Salmon Research Laboratory, Cultus Lake, British Columbia, Canada 5CARRTEL, INRAe, Université de Savoie Mont Blanc, Thonon-les-Bains, France Abstract Paleolimnological studies are central for identifying long-term changes, yet many studies rely on bioindicators that deposit detectable subfossils in sediments, such as diatoms and cladocerans. Emerging DNA-based approaches are expanding the taxonomic diversity that can be investigated. However, as sedimentary DNA-based approaches are expanding rapidly, calibration work is required to determine the advantages and limitations of these tech- niques. In this study, we assessed the congruence between morphological and DNA-based approaches applied to sediment trap samples for diatoms and crustaceans using both intracellular and extracellular DNA. We also evalu- ated which taxa are deposited in sediment traps from the water column to identify potential paleolimnological bioindicators of environmental variations. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Nanoplankton Protists from the Western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)*
sm69n1047 4/3/05 20:30 Página 47 SCI. MAR., 69 (1): 47-74 SCIENTIA MARINA 2005 Nanoplankton protists from the western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)* GIANFRANCO NOVARINO Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, U.K. E-mail: [email protected] SUMMARY: This paper is an electron microscopical account of cryptomonad flagellates (Cryptophyceae = Cryptomon- adea) in the plankton of the western Mediterranean Sea. Bottle samples collected during the spring-summer of 1998 in the Sea of Alboran and Barcelona coastal waters contained a total of eleven photosynthetic species: Chroomonas (sensu aucto- rum) sp., Cryptochloris sp., 3 species of Hemiselmis, 3 species of Plagioselmis including Plagioselmis nordica stat. nov/sp. nov., Rhinomonas reticulata (Lucas) Novarino, Teleaulax acuta (Butcher) Hill, and Teleaulax amphioxeia (Conrad) Hill. Identification was based largely on cell surface features, as revealed by scanning electron microscopy (SEM). Cells were either dispersed in the water-column or associated with suspended particulate matter (SPM). Plagioselmis prolonga was the most common species both in the water-column and in association with SPM, suggesting that it might be a key primary pro- ducer of carbon. Taxonomic keys are given based on SEM. Key words: Cryptomonadea, cryptomonads, Cryptophyceae, flagellates, nanoplankton, taxonomy, ultrastructure. RESUMEN: PROTISTAS NANOPLANCTÓNICOS DEL MAR MEDITERRANEO NOROCCIDENTAL II. CRYPTOMONADALES (CRYPTOPHY- CEAE = CRYPTOMONADEA). – Este estudio describe a los flagelados cryptomonadales (Cryptophyceae = Cryptomonadea) planctónicos del Mar Mediterraneo Noroccidental mediante microscopia electrónica. La muestras recogidas en botellas durante la primavera-verano de 1998 en el Mar de Alboran y en aguas costeras de Barcelona, contenian un total de 11 espe- cies fotosintéticas: Chroomonas (sensu auctorum) sp., Cryptochloris sp., 3 especies de Hemiselmis, 3 especies de Plagio- selmis incluyendo Plagioselmis nordica stat. -
Keynote and Oral Papers1. Algal Diversity and Species Delimitation
European Journal of Phycology ISSN: 0967-0262 (Print) 1469-4433 (Online) Journal homepage: http://www.tandfonline.com/loi/tejp20 Keynote and Oral Papers To cite this article: (2015) Keynote and Oral Papers, European Journal of Phycology, 50:sup1, 22-120, DOI: 10.1080/09670262.2015.1069489 To link to this article: http://dx.doi.org/10.1080/09670262.2015.1069489 Published online: 20 Aug 2015. Submit your article to this journal Article views: 76 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=tejp20 Download by: [University of Kiel] Date: 22 September 2015, At: 02:13 Keynote and Oral Papers 1. Algal diversity and species delimitation: new tools, new insights 1KN.1 1KN.2 HOW COMPLEMENTARY BARCODING AND GENERATING THE DIVERSITY - POPULATION GENETICS ANALYSES CAN UNCOVERING THE SPECIATION HELP SOLVE TAXONOMIC QUESTIONS AT MECHANISMS IN FRESHWATER AND SHORT PHYLOGENETIC DISTANCES: THE TERRESTRIAL MICROALGAE EXAMPLE OF THE BROWN ALGA Š PYLAIELLA LITTORALIS Pavel kaloud ([email protected]) Christophe Destombe1 ([email protected]), Department of Botany, Charles Univrsity in Prague, Alexandre Geoffroy1 ([email protected]), Prague 12801, Czech Republic Line Le Gall2 ([email protected]), Stéphane Mauger3 ([email protected]) and Myriam Valero4 Species are one of the fundamental units of biology, ([email protected]) comparable to genes or cells. Understanding the general patterns and processes of speciation can facilitate the 1Station Biologique de Roscoff, Sorbonne Universités, formulation and testing of hypotheses in the most impor- Université Pierre et Marie Curie, CNRS, Roscoff tant questions facing biology today, including the fitof 29688, France; 2Institut de Systématique, Evolution, organisms to their environment and the dynamics and Biodiversité, UMR 7205 CNRS-EPHE-MNHN-UPMC, patterns of organismal diversity. -
Phylogenomics Invokes the Clade Housing Cryptista, Archaeplastida, and Microheliella Maris
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Phylogenomics invokes the clade housing Cryptista, 2 Archaeplastida, and Microheliella maris. 3 4 Euki Yazaki1, †, *, Akinori Yabuki2, †, *, Ayaka Imaizumi3, Keitaro Kume4, Tetsuo Hashimoto5,6, 5 and Yuji Inagaki6,7 6 7 1: RIKEN iTHEMS, Wako, Saitama 351-0198, Japan 8 2: Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 236-0001, 9 Japan 10 3: College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan. 11 4: Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan 12 5: Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305- 13 8572, Japan 14 6: Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 15 Ibaraki, 305-8572, Japan 16 7: Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, 17 Japan 18 19 †EY and AY equally contributed to this work. 20 *Correspondence addressed to Euki Yazaki: [email protected] and Akinori Yabuki: 21 [email protected] 22 23 Running title: The clade housing Cryptista, Archaeplastida, and Microheliella maris. 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.08.29.458128; this version posted August 31, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Nuclear Genome Sequence of the Plastid-Lacking
Cenci et al. BMC Biology (2018) 16:137 https://doi.org/10.1186/s12915-018-0593-5 RESEARCH ARTICLE Open Access Nuclear genome sequence of the plastid- lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids Ugo Cenci1,2†, Shannon J. Sibbald1,2†, Bruce A. Curtis1,2, Ryoma Kamikawa3, Laura Eme1,2,11, Daniel Moog1,2,12, Bernard Henrissat4,5,6, Eric Maréchal7, Malika Chabi8, Christophe Djemiel8, Andrew J. Roger1,2,9, Eunsoo Kim10 and John M. Archibald1,2,9* Abstract Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea—the first for any goniomonad—to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. Results: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is ~ 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. -
The Ecology and Glycobiology of Prymnesium Parvum
The Ecology and Glycobiology of Prymnesium parvum Ben Adam Wagstaff This thesis is submitted in fulfilment of the requirements of the degree of Doctor of Philosophy at the University of East Anglia Department of Biological Chemistry John Innes Centre Norwich September 2017 ©This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Page | 1 Abstract Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms (HABs) globally, leading to large scale fish kills that have severe ecological and economic implications. A HAB on the Norfolk Broads, U.K, in 2015 caused the deaths of thousands of fish. Using optical microscopy and 16S rRNA gene sequencing of water samples, P. parvum was shown to dominate the microbial community during the fish-kill. Using liquid chromatography-mass spectrometry (LC-MS), the ladder-frame polyether prymnesin-B1 was detected in natural water samples for the first time. Furthermore, prymnesin-B1 was detected in the gill tissue of a deceased pike (Exos lucius) taken from the site of the bloom; clearing up literature doubt on the biologically relevant toxins and their targets. Using microscopy, natural P. parvum populations from Hickling Broad were shown to be infected by a virus during the fish-kill. A new species of lytic virus that infects P. parvum was subsequently isolated, Prymnesium parvum DNA virus (PpDNAV-BW1). -
Extensive Molecular Tinkering in the Evolution of the Membrane Attachment Mode of the Rheb Gtpase
Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase Kristína Záhonová1, Romana Petrželková1, Matus Valach2, Euki Yazaki3, Denis V. Tikhonenkov4, Anzhelika Butenko1, Jan Janouškovec5, Štěpánka Hrdá6, Vladimír Klimeš1, Gertraud Burger2, Yuji Inagaki7, Patrick J. Keeling8, Vladimír Hampl6, Pavel Flegontov1, Vyacheslav Yurchenko1, Marek Eliáš1* 1Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic 2Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada 3Institute for Biological Sciences, University of Tsukuba, Tsukuba, Japan 4Laboratory of Microbiology, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia 5Department of Genetics, Evolution and Environment, University College London, London, United Kingdom 6Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic 7Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan 8Department of Botany, University of British Columbia, Vancouver, Canada *Author for correspondence: Marek Eliáš, Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic, tel.: +420-597092329, e-mail: [email protected] Supplementary Figures S1 to S7 Fig. S1. Phylogenetic analysis confirming identification of Rheb orthologs. The maximum likelihood tree was inferred using RAxML-HPC2 (LG4X+ substitution model) based on a multiple alignment of the conserved GTPase domain (151 aligned amino acid position). The root is arbitrarily placed between the clade comprising bona fide Rhebs and other Ras family proteins. The numbers at branches refer to ML bootstrap values (shown only when ≥65%) and posterior probabilities (≥0.9) calculated using MrBayes (WAG++I substation model). -
AMNH-Scientific-Publications-2014
AMERICAN MUSEUM OF NATURAL HISTORY Fiscal Year 2014 Scientific Publications Division of Anthropology 2 Division of Invertebrate Zoology 11 Division of Paleontology 28 Division of Physical Sciences 39 Department of Earth and Planetary Sciences and Department of Astrophysics Division of Vertebrate Zoology Department of Herpetology 58 Department of Ichthyology 62 Department of Mammalogy 65 Department of Ornithology 78 Center for Biodiversity and Conservation 91 Sackler Institute for Comparative Genomics 99 DIVISION OF ANTHROPOLOGY Berwick, R.C., M.D. Hauser, and I. Tattersall. 2013. Neanderthal language? Just-so stories take center stage. Frontiers in Psychology 4, article 671. Blair, E.H., and Thomas, D.H. 2014. The Guale uprising of 1597: an archaeological perspective from Mission Santa Catalina de Guale (Georgia). In L.M. Panich and T.D. Schneider (editors), Indigenous Landscapes and Spanish Missions: New Perspectives from Archaeology and Ethnohistory: 25–40. Tucson: University of Arizona Press. Charpentier, V., A.J. de Voogt, R. Crassard, J.-F. Berger, F. Borgi, and A. Al- Ma’shani. 2014. Games on the seashore of Salalah: the discovery of mancala games in Dhofar, Sultanate of Oman. Arabian Archaeology and Epigraphy 25: 115– 120. Chowns, T.M., A.H. Ivester, R.L. Kath, B.K. Meyer, D.H. Thomas, and P.R. Hanson. 2014. A New Hypothesis for the Formation of the Georgia Sea Islands through the Breaching of the Silver Bluff Barrier and Dissection of the Ancestral Altamaha-Ogeechee Drainage. Abstract, 63rd Annual Meeting, Geological Society of America, Southeastern Section, April 10–11, 2014. 2 DeSalle, R., and I. Tattersall. 2014. Mr. Murray, you lose the bet.