DOCSLIB.ORG

(12) United States Patent (10) Patent No.: US 6,410,241 B1 Sykes Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(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. 24, shows Similarity to a killer toxin gene of Kluyveromyces 1999, and provisional application No. 60/127,222, filed on lactis,” Yeast, 10:403–414, 1994. Mar. 31, 1999. Buttrick et al., “Behavior of genes directly injected into the (51) Int. Cl." .................................................. C12O 1/68 rat heart in vivo,” Circulation Res., 70:193–198, 1992. (52) U.S. Cl. ........................................... 435/6; 435/7.21 Carlyon et al., “Analysis of the organization of multicopy (58) Field of Search ............................. 435/6, 7.1, 325, linear- and circular-plasmid-carried open reading frames in 435/721; 514/44 Borrelia burgdorferi Sensu lato isolates.” Infect. Immun., 66:1149-1158, 1998. (56) References Cited Court and Bertrand, “Expression of the open reading frames U.S. PATENT DOCUMENTS of a Senescence-inducing, linear mitochondrial plasmid of Neurospora crassa," Plasmid, 30:51–66, 1993. 5,703,057 A * 12/1997 Johnston et al. 6,001,590 A 12/1999 Komeda et al. ........... 435/69.1 Felgner and Liang, “Debugging expression Screening.” 6,143,530 A 11/2000 Crouzet et al. .......... 435/91.42 Nature Biotech., 17:329-330, 1999. 6,280,977 B1 * 8/2001 Liang et al. Griffiths and Yang, “Recombination between heterologous linear and circular mitochondrial plasmids in the fungus FOREIGN PATENT DOCUMENTS Neurospora.” Mol. Gen. Genet, 249:25-36, 1995. EP 2204.82 5/1987 GrZeSzik et al., “Genes encoding the NAD-reducing hydro WO WO 92/08798 5/1992 genase of Rhodococcus opacus MR11, Microbiology, WO WO 93/24639 12/1993 WO WO 96/26270 8/1996 143:1271-1286, 1997. WO WO 97/10345 3/1997 Gusew et al., “Linear DNA must have free ends to transform WO WO 98/21322 * 5/1998 rat cells efficiently,” Mol. Gen. Genet., 206:121–125, 1987. WO WO 98/38296 9/1998 WO WO 99/02671 1/1999 (List continued on next page.) WO WO 99/45130 9/1999 WO WO 99/66053 12/1999 WO WOOO56914 9/2000 Primary Examiner-Remy Yucel ASSistant Examiner Bronwen M. Loeb OTHER PUBLICATIONS (74) Attorney, Agent, or Firm-Fulbright & Jaworski L.L.P. Li et al (1997) Gene Therapy 4:449–454.* (57) ABSTRACT Johnston et al (1997) Vaccine 15: 808–809.* Barry et al (1995) Nature 377. 632–635.* The present invention relates to linear expression elements Logel et al., “Synthesis of crna probes from pcr-generated (LEES) and circular expression elements (CEES), which are dna,” Biotechniques, 13:604–610, 1992. useful in a variety of molecular biology protocols. Cassata et al., “Rapid expression Screening of Caenorhab Specifically, the invention relates to the use of LEEs and ditis elegans homeobox open reading frames using a CEES to Screen for gene function, biological effects of gene two-step polymerase chain reaction promoter-gfp reporter function, antigens, and promoter function. The invention contstruction technique,” Gene, 212:127-135, 1998. also provides methods of producing proteins, antibodies, Johnston and Barry, “Genetic to genomic vaccination,” antigens, and vaccines. Also, the invention relates to meth Vaccine, 15:808–809, 1997. ods of making LEEs and CEES, and LEEs and CEEs Kain et al., “Universal promoter for gene expression without produced by Such methods. cloning: Expression-PCR,” Biotechniques, 10:366-368, 370, 371, 372, 374, 1991. 28 Claims, 8 Drawing Sheets US 6,410,241 B1 Page 2 OTHER PUBLICATIONS Schickel et al., “Kluyveromyces lactis killer system: analysis Haun and MoSS, "Ligation-independent cloning of of cytoplasmic promoters of the linear plasmids, Nucleic. gluthathione S-transferase fusion genes for expression in Acids Res., 24:1879–1886, 1996. Escherichia coli,' Gene, 112:37-43, 1992. Schrinder and Meinhardt, “An extranuclear expression Sys Haun et al., “Rapid, reliable ligation-independent cloning of tem for analysis of cytoplasmic promoters of yeast linear pcr products using modified plasmid vectors, Biotech killer plasmids," Plasmid, 33:139-151, 1995. niques, 13:515-518, 1992. Schinder et al., “Extranuclear expression of the bacterial Kaluz and Flint, “Ligation-independent cloning of PCR Xylose isomerase (XylA) and the UDP-glucose deydroge products with primers containing nonbase residues,” Nucl. nase (hase) genes in yeast with Kluyveromyces lactis linear Acids Res., 22:4845, 1994. killer plasmids as vectors,” Curr. Microbiol., 33:323-330, Kamper et al., “Heterologous gene expression on the linear 1996. DNA killer plasmid from Kluyveromyces lactis,” Curr: Genet., 19:109-118, 1991. Sekine et al., “Identification and characterization of the La Flamme et al., “TrypanoSoma cruzi: expression of inter linear IS3 molecules generated by Staggered breaks,” J. Biol. leukin-2 utilizing both Supercoiled plasmids and linear Chem., 271:197-202, 1996. DNA’s.” Exp. Parasitol., 83:159–163, 1996. Sykes and Johnston, “Linear expression elements: a rapid, in Lobocka et al., “Characterization of the primary immunity Vivo, method to Screen for gene functions,” Nat. Biotech., region of the Escherichia coli linear plasmid prophage 17:355-359, 1999. N15, J. Bacteriol., 178:2902-2910, 1996. Tang et al., “Genetic immunization is a simple method for Mead et al., “A universal method for the direct cloning of eliciting an immune response,” Nature, 356:152-154, 1992, PCR amplified nucleic acid,” Biotechnology, 9:657-663, only pages 152 and 153 provided. 1991. Meinhardt et al., “A novel approach to express a heterolo Tanguy-Rougeau et al., “Expression of a foreign Km' gene gous gene Kluyveromyces lactis linear killer plasmids: in linear killer DNA plasmids in yeast,” Gene., 91:43-50, expression of the bacterial APH gene from a cytoplasmic 1990. promoter fragment without in-phase fusion to the plasmid Ton-Hoang et al., “Efficient transportation of IS911 circles open reading frame,” Plasmid., 32:318-327, 1994. in vitro, Embo. J., 17:1169–1181, 1998. Monoco et al., “Expression of recombinant human granu locyte colony-stimulating factor in CHO dhfr-cells: new Turner and Moyer, “A PCR-based method for manipulation insights into the in vitro amplification expression system.” of the Vaccinia virus genome that eliminates the need for Gene, 180: 145-150, 1996. cloning,” Bio Techniques, 13:764-771, 1992. Rashtchian, "Novel methods for cloning and engineering Xie and Tsong, “Study of mechanisms of electric field-in genes using the polymerase chain reaction, Curr. Opin. duced DNA transfection V. effects of DNA topology on Biotech., 6:30-36, 1995. Surface binding, cell uptake, expression, and integration into Sampath et al., “Versatile vectors for direct cloning and host chromosomes of DNA in the mammalian cell,” BioS ligation-independent cloning of PCR-amplified fragments phys. Jour., 65:1684–1689, 1993. for Surface displays on filamentous bacteriophages, Gene, 190:5-10, 1997. * cited by examiner U.S. Patent Jun. 25, 2002 Sheet 1 of 8 US 6,410,241 B1 bel Ou s MWOd O r S S s s S 901 x suaunt SS U.S. Patent Jun. 25, 2002 Sheet 2 of 8 US 6,410,241 B1 U.S. Patent Jun. 25, 2002 Sheet 3 of 8 US 6,410,241 B1 3OT Sll l/WO &D ?p OU S : d l CY 59G? Oll sC S d bel Ou >< s OOT-IT-IG Q &B l OOTAMO d SSO O wall s s - s s g0l. X sugun1 SS U.S. Patent Jun. 25, 2002 Sheet 4 of 8 US 6,410,241 B1 O r s s s g0l X suaunt 5 U.S. Patent Jun. 25, 2002 Sheet 5 of 8 US 6,410,241 B1 | 0000|| 000||~ 001§ SÈ •) $3 §S. > ~ 0||È U.S. Patent Jun. 25, 2002 Sheet 6 of 8 US 6,410,241 B1 s IAWOd C s S s 601 X suaunt U.S. Patent Jun. 25, 2002 Sheet 8 of 8 US 6,410,241 B1 S S S CS S s S U s CM) Q S. S. S CO CO s CN O apes/7 fu/suallInT Sol US 6,410,241 B1 1 2 METHODS OF SCREENING OPEN READING circular nucleic acid Segment comprising a promoter or FRAMES TO DETERMINE WHETHER THEY putative promoter and an ORF or putative ORF. These ENCODE POLYPEPTDES WITH AN methods may comprise: a) obtaining at least one linear or ABILITY TO GENERATE AN IMMUNE circular nucleic acid Segment comprising a promoter or RESPONSE putative promoter and an ORF encoding a peptide or puta tive ORF; b) placing the nucleic acid segment under con ditions conducive to expression of the polypeptide from the This application claims the benefit of U.S.
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • Author's Manuscript (764.7Kb)
    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.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Unveiling the Role of Rhizaria in the Silicon Cycle Natalia Llopis Monferrer
    Unveiling the role of Rhizaria in the silicon cycle Natalia Llopis Monferrer To cite this version: Natalia Llopis Monferrer. Unveiling the role of Rhizaria in the silicon cycle. Other. Université de Bretagne occidentale - Brest, 2020. English. NNT : 2020BRES0041. tel-03259625 HAL Id: tel-03259625 https://tel.archives-ouvertes.fr/tel-03259625 Submitted on 14 Jun 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE DE DOCTORAT DE L'UNIVERSITE DE BRETAGNE OCCIDENTALE ECOLE DOCTORALE N° 598 Sciences de la Mer et du littoral Spécialité : Chimie Marine Par Natalia LLOPIS MONFERRER Unveiling the role of Rhizaria in the silicon cycle (Rôle des Rhizaria dans le cycle du silicium) Thèse présentée et soutenue à PLouzané, le 18 septembre 2020 Unité de recherche : Laboratoire de Sciences de l’Environnement Marin Rapporteurs avant soutenance : Diana VARELA Professor, Université de Victoria, Canada Giuseppe CORTESE Senior Scientist, GNS Science, Nouvelle Zélande Composition du Jury : Président : Géraldine SARTHOU Directrice de recherche, CNRS, LEMAR, Brest, France Examinateurs : Diana VARELA Professor, Université de Victoria, Canada Giuseppe CORTESE Senior Scientist, GNS Science, Nouvelle Zélande Colleen DURKIN Research Faculty, Moss Landing Marine Laboratories, Etats Unis Tristan BIARD Maître de Conférences, Université du Littoral Côte d’Opale, France Dir.
    [Show full text]
  • A Revised Six-Kingdom System of Life
    Hi ul. R iv. ' 1998,', 73, p p . 203-266 printed in the United Kingdom © Cambridge Philosophical Society 203 A revised six-kingdom system of life T. CAVALIER-SMITH Evolutionary Biology Programme, Canadian Institute for Advanced Research , Department o f Botany , University o f British Columbia, Vancouver, BC, Canada V6T If4 (.Received 27 M arch 1 9 9 6 ; revised 15 December 1 9 9 7 ; accepted 18 December 1997) ABSTRACT A revised six-kingdom system of life is presented, down to the level of infraphylum. As in my 1983 system Bacteria are treated as a single kingdom, and eukaryotes are divided into only five kingdoms: Protozoa, Animalia, Fungi, Plantae and Chromista. Interm ediate high level categories (superkingdom, subkingdom, branch, infrakingdom, supcrphylum, subphylum and infraphylum) arc extensively used lo avoid splitting organisms into an excessive num ber of kingdoms and phyla (60 only being recognized). The two ‘zoological ’ kingdoms. Protozoa and Animalia, are subject to the International Code of Zoological Nomenclature, the kingdom Bacteria to the International Code of Bacteriological Nomenclature, and the three ‘botanical’ kingdoms (Plantae, Fungi, Chromista) lo the International Code of Botanical Nomenclature, Circumscrip­ tions of the kingdoms Bacteria and Plantae remain unchanged since Cavalicr-Smith (1981). The kingdom Fungi is expanded by adding M icrosporidia, because of protein sequence evidence that these amitochondrial intracellular parasites are related to conventional Fungi, not Protozoa. Fungi arc subdivided into four phyla and 20 classes; fungal classification at the rank of subclass and above is comprehensively revised. The kingdoms Protozoa and Animalia are modified in the light of molecular phylogenetic evidence that Myxozoa arc actually Animalia, not Protozoa, and that mesozoans arc related lo bilaterian animals.
    [Show full text]
  • Amoebae and Amoeboid Protists Form a Large and Diverse Assemblage of Eukaryotes Characterized by Various Types of Pseudopodia
    J. Eukaryot. Microbiol., 56(1), 2009 pp. 16–25 r 2009 The Author(s) Journal compilation r 2009 by the International Society of Protistologists DOI: 10.1111/j.1550-7408.2008.00379.x Untangling the Phylogeny of Amoeboid Protists1 JAN PAWLOWSKI and FABIEN BURKI Department of Zoology and Animal Biology, University of Geneva, Geneva, Switzerland ABSTRACT. The amoebae and amoeboid protists form a large and diverse assemblage of eukaryotes characterized by various types of pseudopodia. For convenience, the traditional morphology-based classification grouped them together in a macrotaxon named Sarcodina. Molecular phylogenies contributed to the dismantlement of this assemblage, placing the majority of sarcodinids into two new supergroups: Amoebozoa and Rhizaria. In this review, we describe the taxonomic composition of both supergroups and present their small subunit rDNA-based phylogeny. We comment on the advantages and weaknesses of these phylogenies and emphasize the necessity of taxon-rich multigene datasets to resolve phylogenetic relationships within Amoebozoa and Rhizaria. We show the importance of environmental sequencing as a way of increasing taxon sampling in these supergroups. Finally, we highlight the interest of Amoebozoa and Rhizaria for understanding eukaryotic evolution and suggest that resolving their phylogenies will be among the main challenges for future phylogenomic analyses. Key Words. Amoebae, Amoebozoa, eukaryote, evolution, Foraminifera, Radiolaria, Rhizaria, SSU, rDNA. FROM SARCODINA TO AMOEBOZOA AND RHIZARIA ribosomal genes. The most spectacular fast-evolving lineages, HE amoebae and amoeboid protists form an important part of such as foraminiferans (Pawlowski et al. 1996), polycystines Teukaryotic diversity, amounting for about 15,000 described (Amaral Zettler, Sogin, and Caron 1997), pelobionts (Hinkle species (Adl et al.
    [Show full text]
  • Kingdom Protozoa and Its 18Phyla
    MICROBIOLOGICAL REVIEWS, Dec. 1993, p. 953-994 Vol. 57, No. 4 0146-0749/93/040953-42$02.00/0 Copyright © 1993, American Society for Microbiology Kingdom Protozoa and Its 18 Phyla T. CAVALIER-SMITH Evolutionary Biology Program of the Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 INTRODUCTION .......................................................................... 954 Changing Views of Protozoa as a Taxon.......................................................................... 954 EXCESSIVE BREADTH OF PROTISTA OR PROTOCTISTA ......................................................955 DISTINCTION BETWEEN PROTOZOA AND PLANTAE............................................................956 DISTINCTION BETWEEN PROTOZOA AND FUNGI ................................................................957 DISTINCTION BETWEEN PROTOZOA AND CHROMISTA .......................................................960 DISTINCTION BETWEEN PROTOZOA AND ANIMALIA ..........................................................962 DISTINCTION BETWEEN PROTOZOA AND ARCHEZOA.........................................................962 Transitional Problems in Narrowing the Definition of Protozoa ....................................................963 Exclusion of Parabasalia from Archezoa .......................................................................... 964 Exclusion of Entamoebia from Archezoa .......................................................................... 964 Are Microsporidia
    [Show full text]