BES-‐AG Meeting July 2014
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WO 2016/096923 Al 23 June 2016 (23.06.2016) W P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/096923 Al 23 June 2016 (23.06.2016) W P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 15/82 (2006.01) C12Q 1/68 (2006.01) kind of national protection available): AE, AG, AL, AM, C12N 15/113 (2010.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (21) Number: International Application DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/EP20 15/079893 HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (22) International Filing Date: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, 15 December 2015 (15. 12.2015) MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (25) Filing Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, (26) Publication Language: English TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 14307040.7 15 December 2014 (15. 12.2014) EP kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, (71) Applicants: PARIS SCIENCES ET LETTRES - TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, QUARTIER LATIN [FR/FR]; 62bis, rue Gay-Lussac, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, 75005 Paris (FR). -
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. -
Biology and Systematics of Heterokont and Haptophyte Algae1
American Journal of Botany 91(10): 1508±1522. 2004. BIOLOGY AND SYSTEMATICS OF HETEROKONT AND HAPTOPHYTE ALGAE1 ROBERT A. ANDERSEN Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classi®ed into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed signi®cantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heter- okont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). Key words: chromalveolate; chromist; chromophyte; ¯agella; phylogeny; stramenopile; tree of life. Heterokont algae are a monophyletic group that includes all (Phaeophyceae) by Linnaeus (1753), and shortly thereafter, photosynthetic organisms with tripartite tubular hairs on the microscopic chrysophytes (currently 5 Oikomonas, Anthophy- mature ¯agellum (discussed later; also see Wetherbee et al., sa) were described by MuÈller (1773, 1786). The history of 1988, for de®nitions of mature and immature ¯agella), as well heterokont algae was recently discussed in detail (Andersen, as some nonphotosynthetic relatives and some that have sec- 2004), and four distinct periods were identi®ed. -
Culturable Diversity of Arctic Phytoplankton During Pack Ice
bioRxiv preprint doi: https://doi.org/10.1101/642264; this version posted May 20, 2019. 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-ND 4.0 International license. 1 Culturable diversity of Arctic phytoplankton during pack ice 2 melting 1;2∗ 3;2 4 3 Catherine Gérikas Ribeiro , Adriana Lopes dos Santos , Priscillia Gourvil , 1 1 1 4 4 Florence Le Gall , Dominique Marie , Margot Tragin , Ian Probert , Daniel 1;3 5 Vaulot 1 6 Sorbonne Université, CNRS, UMR7144, Team ECOMAP, Station Biologique de Roscoff, 7 Roscoff, France 2 8 GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Camino La 9 Pirámide, 5750, Huechuraba, Santiago, Chile 3 10 Nanyang Technological University, Asian School of the Environment, Singapore. 4 11 Sorbonne Université, CNRS, FR2424, Roscoff Culture Collection, Station Biologique de 12 Roscoff, Roscoff, France * 13 [email protected] 14 Abstract 15 Massive phytoplankton blooms develop at the Arctic ice edge, sometimes extend- 16 ing far under the pack ice. An extensive culturing effort was conducted before and 17 during a phytoplankton bloom in Baffin Bay between April and July 2016. Differ- 18 ent isolation strategies were applied, including flow cytometry cell sorting, man- 19 ual single cell pipetting and serial dilution. Although all three techniques yielded 20 the most common organisms, each technique retrieved specific taxa, highlight- 21 ing the importance of using several methods to maximize the number and diver- 22 sity of isolated strains. -
Guy Hällfors
Baltic Sea Environment Proceedings No. 95 Checklist of Baltic Sea Phytoplankton Species Helsinki Commission Baltic Marine Environment Protection Commission 2004 Guy Hällfors Checklist of Baltic Sea Phytoplankton Species (including some heterotrophic protistan groups) 4 Checklist of Baltic Sea Phytoplankton Species (including some heterotrophic protistan groups) Guy Hällfors Finnish Institute of Marine Research P.O. Box 33 (Asiakkaankatu 3) 00931 Helsinki Finland E-mail: guy.hallfors@fi mr.fi On the cover: The blue-green alga Anabaena lemmermannii. Photo Seija Hällfors / FIMR Introduction 5 Two previous checklists of Baltic Sea phytoplankton (Hällfors 1980 (1979) and Edler et al. 1984) were titled ”preliminary”. Our knowledge of the taxonomy and distribution of Baltic Sea phytoplankton has increased considerably over the last 20 years. Much of this new information has been incorporated in this new list. Data from a number of older publications overlooked by Edler et al. (1984) has also been included. As a result, the number of species included has grown considerably. Especially the inclusion of more estuarine species adapted to salinities lower than those of the open Baltic Sea has increased the number of species. The new list also contains species which mainly grow in ice but form sparse planktonic populations in the beginning of the spring bloom, and species of benthic or littoral origin (whether epiphytic, epilitic, epipsammic, epipelic, or rarely epizooic), that are occasionally found in the plankton. The benthic and littoral species are coded with an ”l” in the checklist. Concerning the diatoms, especially in the order Bacillariales, it is usually impossible to tell whether the cells of such species have been alive when sampled because of the preparation techniques (including the removal of cell contents) required for an accurate determination. -
Systema Naturae. the Classification of Living Organisms
Systema Naturae. The classification of living organisms. c Alexey B. Shipunov v. 5.601 (June 26, 2007) Preface Most of researches agree that kingdom-level classification of living things needs the special rules and principles. Two approaches are possible: (a) tree- based, Hennigian approach will look for main dichotomies inside so-called “Tree of Life”; and (b) space-based, Linnaean approach will look for the key differences inside “Natural System” multidimensional “cloud”. Despite of clear advantages of tree-like approach (easy to develop rules and algorithms; trees are self-explaining), in many cases the space-based approach is still prefer- able, because it let us to summarize any kinds of taxonomically related da- ta and to compare different classifications quite easily. This approach also lead us to four-kingdom classification, but with different groups: Monera, Protista, Vegetabilia and Animalia, which represent different steps of in- creased complexity of living things, from simple prokaryotic cell to compound Nature Precedings : doi:10.1038/npre.2007.241.2 Posted 16 Aug 2007 eukaryotic cell and further to tissue/organ cell systems. The classification Only recent taxa. Viruses are not included. Abbreviations: incertae sedis (i.s.); pro parte (p.p.); sensu lato (s.l.); sedis mutabilis (sed.m.); sedis possi- bilis (sed.poss.); sensu stricto (s.str.); status mutabilis (stat.m.); quotes for “environmental” groups; asterisk for paraphyletic* taxa. 1 Regnum Monera Superphylum Archebacteria Phylum 1. Archebacteria Classis 1(1). Euryarcheota 1 2(2). Nanoarchaeota 3(3). Crenarchaeota 2 Superphylum Bacteria 3 Phylum 2. Firmicutes 4 Classis 1(4). Thermotogae sed.m. 2(5). -
Observing Life in the Sea
May 24, 2019 Observing Life in the Sea Sanctuaries MBON Monterey Bay, Florida Keys, and Flower Garden Banks National Marine Sanctuaries Principal Investigators: Frank Muller-Karger (USF) Francisco Chávez (MBARI) Illustration by Kelly Lance© 2016 MBARI Partners: E. Montes/M. Breitbart/A. Djurhuus/N. Sawaya1, K. Pitz/R. Michisaki2, Maria Kavanaugh3, S. Gittings/A. Bruckner/K. Thompson4, B.Kirkpatrick5, M. Buchman6, A. DeVogelaere/J. Brown7, J. Field8, S. Bograd8, E. Hazen8, A. Boehm9, K. O'Keife/L. McEachron10, G. Graettinger11, J. Lamkin12, E. (Libby) Johns/C. Kelble/C. Sinigalliano/J. Hendee13, M. Roffer14 , B. Best15 Sanctuaries MBON 1 College of Marine Science, Univ. of South Florida (USF), St Petersburg, FL; 2 MBARI/CenCOOS, CA; 3 Oregon State University, Corvallis, OR; 4 NOAA Office of National Marine Sanctuaries (ONMS), Washington, DC; 5 Texas A&M University (TAMU/GCOOS), College Station, TX; Monterey Bay, 6 NOAA Florida Keys National Marine Sanctuary (FKNMS), Key West, FL; Florida Keys, and 7 NOAA Monterey Bay National Marine Sanct. (MBNMS), Monterey, CA; Flower Garden Banks 8 NOAA SW Fisheries Science Center (SWFSC), La Jolla, CA, 9 Center for Ocean Solutions, Stanford University, Pacific Grove, CA; National Marine Sanctuaries 10 Florida Fish and Wildlife Research Institute (FWRI), St Petersburg, FL; 11NOAA Office of Response and Restoration (ORR), Seattle, WA; Principal Investigators: 12NOAA SE Fisheries Science Center (SEFSC), Miami, FL; Frank Muller-Karger (USF) 13NOAA Atlantic Oceanographic and Meteorol. Lab. (AOML), Miami, -
Kingdom Chromista)
J Mol Evol (2006) 62:388–420 DOI: 10.1007/s00239-004-0353-8 Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista) Thomas Cavalier-Smith, Ema E-Y. Chao Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK Received: 11 December 2004 / Accepted: 21 September 2005 [Reviewing Editor: Patrick J. Keeling] Abstract. Heterokonts are evolutionarily important gyristea cl. nov. of Ochrophyta as once thought. The as the most nutritionally diverse eukaryote supergroup zooflagellate class Bicoecea (perhaps the ancestral and the most species-rich branch of the eukaryotic phenotype of Bigyra) is unexpectedly diverse and a kingdom Chromista. Ancestrally photosynthetic/ major focus of our study. We describe four new bicil- phagotrophic algae (mixotrophs), they include several iate bicoecean genera and five new species: Nerada ecologically important purely heterotrophic lineages, mexicana, Labromonas fenchelii (=Pseudobodo all grossly understudied phylogenetically and of tremulans sensu Fenchel), Boroka karpovii (=P. uncertain relationships. We sequenced 18S rRNA tremulans sensu Karpov), Anoeca atlantica and Cafe- genes from 14 phagotrophic non-photosynthetic het- teria mylnikovii; several cultures were previously mis- erokonts and a probable Ochromonas, performed ph- identified as Pseudobodo tremulans. Nerada and the ylogenetic analysis of 210–430 Heterokonta, and uniciliate Paramonas are related to Siluania and revised higher classification of Heterokonta and its Adriamonas; this clade (Pseudodendromonadales three phyla: the predominantly photosynthetic Och- emend.) is probably sister to Bicosoeca. Genetically rophyta; the non-photosynthetic Pseudofungi; and diverse Caecitellus is probably related to Anoeca, Bigyra (now comprising subphyla Opalozoa, Bicoecia, Symbiomonas and Cafeteria (collectively Anoecales Sagenista). The deepest heterokont divergence is emend.). Boroka is sister to Pseudodendromonadales/ apparently between Bigyra, as revised here, and Och- Bicoecales/Anoecales. -
Influence of Sea Ice on Protist Community Structure in the Central Arctic Ocean
Table of Contents Influence of sea ice on protist community structure in the Central Arctic Ocean by Kristin Hardge A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology Approved Dissertation Committee: Dr. Katja Metfies1, 2 Prof. Dr. Matthias Ullrich1 Dr. Mona Hoppenrath3 Dr. Eva-Maria Nöthig2 1 Jacobs University Bremen 2 Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 3 Senckenberg Research Institute, German Centre for Marine Biodiversity Research, Wilhelmshaven Date of Defense: 10 August 2016 1 Table of Contents 2 Table of Contents “In the case of all things which have several parts and in which the totality is not, as it were, a mere heap, but the whole is something besides the parts, there is a cause.” Aristotle, Metaphysics 3 Table of Contents 4 Table of Contents Table of Contents 1 Summary ....................................................................................................................................... 7 2 General Introduction ..................................................................................................................... 9 2.1 Global warming ....................................................................................................................... 9 2.2 Changes in Arctic sea ice ........................................................................................................ 9 2.3 Protist biodiversity in the Arctic Ocean ............................................................................... -
Climate Change in the Arctic Extended Abstracts Reykjavik, Iceland November 9-12, 2004 Climate Change in the Arctic
Arctic Climate Impact Assessment (ACIA) AMAP Report 2004:4 The ACIA International Scientific Symposium on The ACIA International Scientific Symposium on ACIA The Climate Change The ACIA International in the Arctic Scientific Symposium on Climate Change in the Arctic Extended Abstracts Reykjavik, Iceland November 9-12, 2004 Climate Change in the Arctic Climate Change in the ISBN 82-7971-041-8 AMAP Extended Abstracts Report 2004:4 Reykjavik, Iceland. November 9-12, 2004 GUTENBERG 26739 The ACIA Symposium is organized by: Arctic Monitoring and Assessment Programme (AMAP) Conservation of Arctic Flora and Fauna (CAFF) International Arctic Science Committee (IASC) ACIA Secretariat The ACIA Symposium is sponsored by: Arctic Monitoring and Assessment Programme (AMAP) Environment Canada Finnish Ministry of the Environment Icelandic Ministry of the Environment Icelandic Ministry of Foreign Affairs International Arctic Science Committee (IASC) Nordic Council of Ministers Norwegian Ministry of the Environment Norwegian Ministry of Foreign Affairs The ACIA International Scientific Symposium on Climate Change in the Arctic: Standing Committee of Arctic Parliamentarians Extended Abstracts. Reykjavik, Iceland, 9-12 November 2004. AMAP Report 2004:4 Swedish Environmental Protection Agency U.S. National Oceanic and Atmospheric Administration (NOAA) © Arctic Monitoring and Assessment Programme (AMAP), Oslo, Norway. U.S. State Department October 2004. World Wide Fund for Nature ISBN 82-7971-041-8 The ACIA Symposium is supported by: Environment and Food Agency -
The Revised Classification of Eukaryotes
Published in Journal of Eukaryotic Microbiology 59, issue 5, 429-514, 2012 which should be used for any reference to this work 1 The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. MITCHELL,l SHARON E. MOZLEY-STANRIDGE,p LAURA W. PARFREY,q JAN PAWLOWSKI,r SONJA RUECKERT,s LAURA SHADWICK,t CONRAD L. SCHOCH,u ALEXEY SMIRNOVv and FREDERICK W. SPIEGELt aDepartment of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada, and bDepartment of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and cDepartment of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA, and dBiology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, Cˇeske´ Budeˇjovice, Czech Republic, and eZoology Department, Natural History Museum, London, SW7 5BD, United Kingdom, and fWadsworth Center, New York State Department of Health, Albany, New York, 12201, USA, and gDepartment of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and hDepartment of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and iDepartment of Ecology, University of Kaiserslautern, 67663, Kaiserslautern, Germany, and jDepartment of Parasitology, Charles University, Prague, 128 43, Praha 2, Czech -
Adl S.M., Simpson A.G.B., Lane C.E., Lukeš J., Bass D., Bowser S.S
The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. MITCHELL,l SHARON E. MOZLEY-STANRIDGE,p LAURA W. PARFREY,q JAN PAWLOWSKI,r SONJA RUECKERT,s LAURA SHADWICK,t CONRAD L. SCHOCH,u ALEXEY SMIRNOVv and FREDERICK W. SPIEGELt aDepartment of Soil Science, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada, and bDepartment of Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and cDepartment of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA, and dBiology Center and Faculty of Sciences, Institute of Parasitology, University of South Bohemia, Cˇeske´ Budeˇjovice, Czech Republic, and eZoology Department, Natural History Museum, London, SW7 5BD, United Kingdom, and fWadsworth Center, New York State Department of Health, Albany, New York, 12201, USA, and gDepartment of Biochemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada, and hDepartment of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada, and iDepartment