Distribution Patterns of the Radiolarian Nuclei and Symbionts Using DAPI-Fluorescence
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Molecular Phylogenetic Position of Hexacontium Pachydermum Jørgensen (Radiolaria)
Marine Micropaleontology 73 (2009) 129–134 Contents lists available at ScienceDirect Marine Micropaleontology journal homepage: www.elsevier.com/locate/marmicro Molecular phylogenetic position of Hexacontium pachydermum Jørgensen (Radiolaria) Tomoko Yuasa a,⁎, Jane K. Dolven b, Kjell R. Bjørklund b, Shigeki Mayama c, Osamu Takahashi a a Department of Astronomy and Earth Sciences, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan b Natural History Museum, University of Oslo, P.O. Box 1172, Blindern, 0318 Oslo, Norway c Department of Biology, Tokyo Gakugei University, Koganei, Tokyo 184-8501, Japan article info abstract Article history: The taxonomic affiliation of Hexacontium pachydermum Jørgensen, specifically whether it belongs to the Received 9 April 2009 order Spumellarida or the order Entactinarida, is a subject of ongoing debate. In this study, we sequenced the Received in revised form 3 August 2009 18S rRNA gene of H. pachydermum and of three spherical spumellarians of Cladococcus viminalis Haeckel, Accepted 7 August 2009 Arachnosphaera myriacantha Haeckel, and Astrosphaera hexagonalis Haeckel. Our molecular phylogenetic analysis revealed that the spumellarian species of C. viminalis, A. myriacantha, and A. hexagonalis form a Keywords: monophyletic group. Moreover, this clade occupies a sister position to the clade comprising the spongodiscid Radiolaria fi Entactinarida spumellarians, coccodiscid spumellarians, and H. pachydermum. This nding is contrary to the results of Spumellarida morphological studies based on internal spicular morphology, placing H. pachydermum in the order Nassellarida Entactinarida, which had been considered to have a common ancestor shared with the nassellarians. 18S rRNA gene © 2009 Elsevier B.V. All rights reserved. Molecular phylogeny. 1. Introduction the order Entactinarida has an inner spicular system homologenous with that of the order Nassellarida. -
Optics-Based Surveys of Large Unicellular Zooplankton: a Case Study on Radiolarians and Phaeodarians
Plankton Benthos Res 12(2): 95–103, 2017 Plankton & Benthos Research © The Plankton Society of Japan Optics-based surveys of large unicellular zooplankton: a case study on radiolarians and phaeodarians 1, 2 3 4,5 YASUHIDE NAKAMURA *, REI SOMIYA , NORITOSHI SUZUKI , MITSUKO HIDAKA-UMETSU , 6 4,5 ATSUSHI YAMAGUCHI & DHUGAL J. LINDSAY 1 Department of Botany, National Museum of Nature and Science, Tsukuba 305–0005, Japan 2 Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852–8521, Japan 3 Department of Earth Science, Graduate School of Science, Tohoku University, Sendai 980–8578, Japan 4 Research and Development (R&D) Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka 237–0061, Japan 5 School of Marine Biosciences, Kitasato University, Sagamihara 252–0373, Japan 6 Graduate School of Fisheries Sciences, Hokkaido University, Hakodate 041–8611, Japan Received 24 May 2016; Accepted 6 February 2017 Responsible Editor: Akihiro Tuji Abstract: Optics-based surveys for large unicellular zooplankton were carried out in five different oceanic areas. New identification criteria, in which “radiolarian-like plankton” are categorized into nine different groups, are proposed for future optics-based surveys. The autonomous visual plankton recorder (A-VPR) captured 65 images of radiolarians (three orders: Acantharia, Spumellaria and Collodaria) and 117 phaeodarians (four taxa: Aulacanthidae, Phaeosphaeri- da, Tuscaroridae and Coelodendridae). Colonies were observed for one radiolarian order (Collodaria) and three phae- odarian taxa (Phaeosphaerida, Tuscaroridae and Coelodendridae). The rest of the radiolarian orders (Taxopodia and Nassellaria) and the other phaeodarian taxa were not detected because of their small cell size (< ca. -
(12) United States Patent (10) Patent No.: US 6,410,241 B1 Sykes Et Al
US006410241B1 (12) United States Patent (10) Patent No.: US 6,410,241 B1 Sykes et al. (45) Date of Patent: Jun. 25, 2002 (54) METHODS OF SCREENING OPEN READING Nisson et al., “Rapid and efficient cloning of Alu-PCR FRAMES TO DETERMINE WHETHER THEY products using uracil DNA glycosylase,” PCR Methods ENCODE POLYPEPTIDES WITH AN Appl., 1:120-123, 1991. ABILITY TO GENERATE AN IMMUNE Rashtchian et al., “Uracil DNA glycosylase-mediated clon RESPONSE ing of polymerase chain reaction-amplified DNA. Applica tion to genomic and cDNA cloning,” Anal. Biochem, (75) Inventors: Kathryn F. Sykes; Stephen Albert 206:91-97, 1992. Johnston, both of Dallas, TX (US) Switzer et al., “Rapid Screening of open reading frames by (73) Assignee: Board of Regents, The University of protein Synthesis with an in Vitro transcription and transla Texas System, Austin, TX (US) tion assay,” Biotechniques, 18:244-248, 1995. ASlanidis and Jong, "Ligation-independent cloning of PCR (*) Notice: Subject to any disclaimer, the term of this products (LIC-PCR).” Nucl. Acids Res., 18:6069–6074, patent is extended or adjusted under 35 1990. U.S.C. 154(b) by 0 days. ASlanidis et al., “Minimal length requirement of the Sin gle-stranded tails for ligation-independent cloning (LIC) of (21) Appl. No.: 09/535,366 pcr products.” PCR Methods and Applications, 4:172-177, (22) Filed: Mar. 24, 2000 1994. Bolen et al., “Isolation and Sequence analysis of a gene from Related U.S. Application Data the linear DNA plasmid pPacl-2 of pichia acaciae that (60) Provisional application No. 60/125,864, filed on Mar. -
Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
Radiozoa (Acantharia, Phaeodaria and Radiolaria) and Heliozoa
MICC16 26/09/2005 12:21 PM Page 188 CHAPTER 16 Radiozoa (Acantharia, Phaeodaria and Radiolaria) and Heliozoa Cavalier-Smith (1987) created the phylum Radiozoa to Radiating outwards from the central capsule are the include the marine zooplankton Acantharia, Phaeodaria pseudopodia, either as thread-like filopodia or as and Radiolaria, united by the presence of a central axopodia, which have a central rod of fibres for rigid- capsule. Only the Radiolaria including the siliceous ity. The ectoplasm typically contains a zone of frothy, Polycystina (which includes the orders Spumellaria gelatinous bubbles, collectively termed the calymma and Nassellaria) and the mixed silica–organic matter and a swarm of yellow symbiotic algae called zooxan- Phaeodaria are preserved in the fossil record. The thellae. The calymma in some spumellarian Radiolaria Acantharia have a skeleton of strontium sulphate can be so extensive as to obscure the skeleton. (i.e. celestine SrSO4). The radiolarians range from the A mineralized skeleton is usually present within the Cambrian and have a virtually global, geographical cell and comprises, in the simplest forms, either radial distribution and a depth range from the photic zone or tangential elements, or both. The radial elements down to the abyssal plains. Radiolarians are most useful consist of loose spicules, external spines or internal for biostratigraphy of Mesozoic and Cenozoic deep sea bars. They may be hollow or solid and serve mainly to sediments and as palaeo-oceanographical indicators. support the axopodia. The tangential elements, where Heliozoa are free-floating protists with roughly present, generally form a porous lattice shell of very spherical shells and thread-like pseudopodia that variable morphology, such as spheres, spindles and extend radially over a delicate silica endoskeleton. -
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1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. -
VII EUROPEAN CONGRESS of PROTISTOLOGY in Partnership with the INTERNATIONAL SOCIETY of PROTISTOLOGISTS (VII ECOP - ISOP Joint Meeting)
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/283484592 FINAL PROGRAMME AND ABSTRACTS BOOK - VII EUROPEAN CONGRESS OF PROTISTOLOGY in partnership with THE INTERNATIONAL SOCIETY OF PROTISTOLOGISTS (VII ECOP - ISOP Joint Meeting) Conference Paper · September 2015 CITATIONS READS 0 620 1 author: Aurelio Serrano Institute of Plant Biochemistry and Photosynthesis, Joint Center CSIC-Univ. of Seville, Spain 157 PUBLICATIONS 1,824 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Use Tetrahymena as a model stress study View project Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica View project All content following this page was uploaded by Aurelio Serrano on 04 November 2015. The user has requested enhancement of the downloaded file. VII ECOP - ISOP Joint Meeting / 1 Content VII ECOP - ISOP Joint Meeting ORGANIZING COMMITTEES / 3 WELCOME ADDRESS / 4 CONGRESS USEFUL / 5 INFORMATION SOCIAL PROGRAMME / 12 CITY OF SEVILLE / 14 PROGRAMME OVERVIEW / 18 CONGRESS PROGRAMME / 19 Opening Ceremony / 19 Plenary Lectures / 19 Symposia and Workshops / 20 Special Sessions - Oral Presentations / 35 by PhD Students and Young Postdocts General Oral Sessions / 37 Poster Sessions / 42 ABSTRACTS / 57 Plenary Lectures / 57 Oral Presentations / 66 Posters / 231 AUTHOR INDEX / 423 ACKNOWLEDGMENTS-CREDITS / 429 President of the Organizing Committee Secretary of the Organizing Committee Dr. Aurelio Serrano -
Distribution Patterns of the Radiolarian Nuclei and Symbionts Using DAPI-Fluorescence
Bull. Natl. Mus. Nat. Sci., Ser. B, 35(4), pp. 169–182, December 22, 2009 Distribution Patterns of the Radiolarian Nuclei and Symbionts Using DAPI-Fluorescence Noritoshi Suzuki1*, Kaoru Ogane1,9, Yoshiaki Aita2, Mariko Kato3, Saburo Sakai4, Toshiyuki Kurihara5, Atsushi Matsuoka6, Susumu Ohtsuka7, Akio Go8, Kazumitsu Nakaguchi8, Shuhei Yamaguchi8, Takashi Takahashi7 and Akihiro Tuji9 1 Institute of Geology and Paleontology, Graduate School of Science, Tohoku University, Aoba 6–3, Aramaki, Aoba-ku, Sendai, 980–8578 Japan 2 Department of Geology, Faculty of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, 321–8505 Japan 3 Plant Science, Graduate School of Agricultural Science, Utsunomiya University, Mine-machi 350, Utsunomiya, 321–8505 Japan 4 Institute of Biogeoscience, JAMSTEC, Natsushima-cho 2–15, Yokosuka, 237–0061 Japan 5 Graduate School of Science and Technology, Niigata University, Niigata, 950–2181 Japan 6 Department of Geology, Faculty of Science, Niigata University, Niigata, 950–2181 Japan 7 Takehara Marine Science Station, Setouchi Field Science Center, Graduate School of Biosphere Science, Hiroshima University, Minato-machi 5–8–1, Takehara, Hiroshima, 725–0024 Japan 8 Faculty of Applied Biological Science, Hiroshima University, Kagamiyama 1–4–4, Higashi-Hiroshima, 739–8528 Japan 9 Department of Botany, National Museum of Nature and Science, Amakubo 4–1–1, Tsukuba, 305–0005 Japan * E-mail: [email protected] Abstract This study is the first report on the successful application of the DAPI (4Ј,6-diamidino- 2-phenylindole) staining technique to 22 families of five of the six radiolarian orders (Acantharia, Collodaria, Nassellaria, Spumellaria, and Taxopodia, excluding Entactinaria). A total of six Acan- tharian species, three Collodarian species, three Spumellarian species, 18 Nassellarian species, and one Taxopod species emitted blue light under epifluorescence microscopy after DAPI staining. -
The Horizontal Distribution of Siliceous Planktonic Radiolarian Community in the Eastern Indian Ocean
water Article The Horizontal Distribution of Siliceous Planktonic Radiolarian Community in the Eastern Indian Ocean Sonia Munir 1 , John Rogers 2 , Xiaodong Zhang 1,3, Changling Ding 1,4 and Jun Sun 1,5,* 1 Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; [email protected] (S.M.); [email protected] (X.Z.); [email protected] (C.D.) 2 Research School of Earth Sciences, Australian National University, Acton 2601, Australia; [email protected] 3 Department of Ocean Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong 4 College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China 5 College of Marine Science and Technology, China University of Geosciences, Wuhan 430074, China * Correspondence: [email protected]; Tel.: +86-606-011-16 Received: 9 October 2020; Accepted: 3 December 2020; Published: 13 December 2020 Abstract: The plankton radiolarian community was investigated in the spring season during the two-month cruise ‘Shiyan1’ (10 April–13 May 2014) in the Eastern Indian Ocean. This is the first comprehensive plankton tow study to be carried out from 44 sampling stations across the entire area (80.00◦–96.10◦ E, 10.08◦ N–6.00◦ S) of the Eastern Indian Ocean. The plankton tow samples were collected from a vertical haul from a depth 200 m to the surface. During the cruise, conductivity–temperature–depth (CTD) measurements were taken of temperature, salinity and chlorophyll a from the surface to 200 m depth. Shannon–Wiener’s diversity index (H’) and the dominance index (Y) were used to analyze community structure. -
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). -
Protista (PDF)
1 = Astasiopsis distortum (Dujardin,1841) Bütschli,1885 South Scandinavian Marine Protoctista ? Dingensia Patterson & Zölffel,1992, in Patterson & Larsen (™ Heteromita angusta Dujardin,1841) Provisional Check-list compiled at the Tjärnö Marine Biological * Taxon incertae sedis. Very similar to Cryptaulax Skuja Laboratory by: Dinomonas Kent,1880 TJÄRNÖLAB. / Hans G. Hansson - 1991-07 - 1997-04-02 * Taxon incertae sedis. Species found in South Scandinavia, as well as from neighbouring areas, chiefly the British Isles, have been considered, as some of them may show to have a slightly more northern distribution, than what is known today. However, species with a typical Lusitanian distribution, with their northern Diphylleia Massart,1920 distribution limit around France or Southern British Isles, have as a rule been omitted here, albeit a few species with probable norhern limits around * Marine? Incertae sedis. the British Isles are listed here until distribution patterns are better known. The compiler would be very grateful for every correction of presumptive lapses and omittances an initiated reader could make. Diplocalium Grassé & Deflandre,1952 (™ Bicosoeca inopinatum ??,1???) * Marine? Incertae sedis. Denotations: (™) = Genotype @ = Associated to * = General note Diplomita Fromentel,1874 (™ Diplomita insignis Fromentel,1874) P.S. This list is a very unfinished manuscript. Chiefly flagellated organisms have yet been considered. This * Marine? Incertae sedis. provisional PDF-file is so far only published as an Intranet file within TMBL:s domain. Diplonema Griessmann,1913, non Berendt,1845 (Diptera), nec Greene,1857 (Coel.) = Isonema ??,1???, non Meek & Worthen,1865 (Mollusca), nec Maas,1909 (Coel.) PROTOCTISTA = Flagellamonas Skvortzow,19?? = Lackeymonas Skvortzow,19?? = Lowymonas Skvortzow,19?? = Milaneziamonas Skvortzow,19?? = Spira Skvortzow,19?? = Teixeiromonas Skvortzow,19?? = PROTISTA = Kolbeana Skvortzow,19?? * Genus incertae sedis. -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878.