The Effect of Enucleation on Flagellar Regeneration in the Protozoon Peranema Trichophorum
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A Morphological Re-Description of Ploeotia Pseudanisonema, and Phylogenetic Analysis of the Genus Ploeotia
A Morphological Re-Description of Ploeotia pseudanisonema, and Phylogenetic Analysis of the Genus Ploeotia by Andrew Buren Brooks (Under the direction of Mark A. Farmer) Abstract The genus Ploeotia represents a group of small, colorless, heterotrophic euglenids commonly found in shallow-water marine sediments. Species belonging to this genus have histori- cally been poorly described and studied. However, a Group I intron discovered within the small subunit ribosomal DNA gene of Ploeotia costata, makes P. costata the only euglena- zoan known to possess an actively splicing Group I intron. This intron contains conserved secondary structures that indicate monophyly with introns found in Stramenopiles and Ban- giales red algae. This project describes the internal and external morphology of a related species, Ploeotia pseudanisonema, using light and electron microscopy, and investigates the possibility of a Group I intron within P. pseudanisonema. Using recently obtained SSU rRNA sequences, we also examine the phylogeny of Ploeotia, and comment on the relationship of the genus Keelungia to Ploeotia. Index words: Ploeotia pseudanisonema, Ploeotia costata, Ploeotia vitrea, Keelungia pulex, Transmission electron microscopy, Scanning electron microscopy, Small subunit rRNA, Euglenozoan Phylogeny A Morphological Re-Description of Ploeotia pseudanisonema, and Phylogenetic Analysis of the Genus Ploeotia by Andrew Buren Brooks B.S., University of Alabama, 2009 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree Master of Science Athens, Georgia 2010 c 2014 Andrew Buren Brooks All Right Reserved A Morphological Re-Description of Ploeotia pseudanisonema, and Phylogenetic Analysis of the Genus Ploeotia by Andrew Buren Brooks Approved: Major Professor: Mark A. -
Eukaryotes Microbes
rator abo y M L ic ve ro IV Eukaryote Microbes 1–7 ti b c i a o r l o e t g y n I 1 Algae, 2 Lichens, 3 Fungi, I I I I I I I I I I I B 4 Fleshy Fungi, 5 Protozoa, s a e s c ic n , A ie 6 Slime Molds, 7 Water Molds p Sc pl h ied & Healt Eukaryotes 1 Algae top of page ● Objectives/Key Words ✟ 9 motility & structure videos ● Algal Thallus ✟ Carpenter’s diatom motility ● Algal Wet Mount (Biosafety Level 1)✲✱✓ ✟ Chlamydomonas motility ● Algal Wet Mount (Biosafety Level 2)✲✱✓ ✟ Diatom gliding movement ● Algal Wet Mount (disposable loop) ✲✱✱✓ ✟ Euglena motility ● Microscopic Algae✓ ✟ Gyrosigma motility ✟ ❍ Green Algae (Chlorophyta) ✟ Noctiluca scintillans motility ✟ ❍ Chlamydomonas ✟ Peridinium dinoflagellate motility ✟ ❍ Euglenoids (Euglenophyta) ✟ Synura cells & colony ❍ Diatoms (Chrysophyta) ✟ Volvox flagellate cells ✟✟ ❍ 1 frustules & motility ◆ ❍ 2 cell division ❖14 scenic microbiology, 60 images, 9 videos ❍ 3 sexual reproduction ❖ Biofouling 1, 2 ❍ 4 striae ❖ Coral Bleaching: Hawaii ✟◆ ◆ Volvox ❍ Dinoflagellates (Pyrrophyta) ❖ Coral Reefs: Pacific Ocean ❍ Red Tide 1–2 ❖ Coral Reefs 2: Andaman Sea, Indian Ocean◆ ❖ “Doing the Laundry”, India◆◆ ● Eukaryotes Quick Quiz 1A: Algae ❖ Green Lake, Lanzarote◆ ● Eukaryotes Quick Quiz 1B: Best Practice ❖ Garden Pond, British Columbia Canada, 1◆, 2 ● Eukaryotes Question Bank1.1✓–1.16◆◆◆◆◆◆◆◆✟✟✟ ❖ Marine Luminescence, Sucia Island, WA, US◆ ❖ Red Tide, Vancouver & Comox, Canada ● 35 interactive pdf pages ❖ Sea Turtle Tracks, Galápagos Islands◆ ● 112 illustrations, 80 images of algae ❖ Sea Turtles & Sea -
Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. -
Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
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). -
Pusillus Poseidon's Guide to Protozoa
Pusillus Poseidon’s guide to PROTOZOA GENERAL NOTES ABOUT PROTOZOANS Protozoa are also called protists. The word “protist” is the more general term and includes all types of single-celled eukaryotes, whereas “protozoa” is more often used to describe the protists that are animal-like (as opposed to plant-like or fungi-like). Protists are measured using units called microns. There are 1000 microns in one millimeter. A millimeter is the smallest unit on a metric ruler and can be estimated with your fingers: The traditional way of classifying protists is by the way they look (morphology), by the way they move (mo- tility), and how and what they eat. This gives us terms such as ciliates, flagellates, ameboids, and all those colors of algae. Recently, the classification system has been overhauled and has become immensely complicated. (Infor- mation about DNA is now the primary consideration for classification, rather than how a creature looks or acts.) If you research these creatures on Wikipedia, you will see this new system being used. Bear in mind, however, that the categories are constantly shifting as we learn more and more about protist DNA. Here is a visual overview that might help you understand the wide range of similarities and differences. Some organisms fit into more than one category and some don’t fit well into any category. Always remember that classification is an artificial construct made by humans. The organisms don’t know anything about it and they don’t care what we think! CILIATES Eats anything smaller than Blepharisma looks slightly pink because it Blepharisma itself, even smaller Bleph- makes a red pigment that senses light (simi- arismas. -
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). -
Chasmostoma Massart, 1920 and Jenningsia Schaeffer, 1918
Protistology 1, 10-16 (1999) Protistology April, 1999 Australian records of two lesser known genera of heterotrophic euglenids – Chasmostoma Massart, 1920 and Jenningsia Schaeffer, 1918 W.J. Lee, R. Blackmore and D.J. Patterson School of Biological Sciences, University of Sydney, NSW 2006, Australia. Summary We report on Chasmostoma and Jenningsia, two genera of heterotrophic euglenids which have not been reported subsequent to their initial descriptions. Chasmostoma nieuportense was poorly described from Belgian coastal waters by Massart in 1920. A redescription is offered on the basis of material observed in a prawn farm in Queensland, Australia. The genus is distinguished by having an anterior cavity into which the flagellum may be withdrawn when the organism is challenged. Jenningsia is a peranemid genus described with a single emergent flagellum by Shaeffer in 1918. The genus was later redescribed by Lackey in 1940 as Peranemopsis. The recent assumptions that these authors overlooked a second flagellum now seem to be in error, and we assign organisms previously described as Peranema fusiforme and P. macrostoma, species of Peranema described with one emergent flagellum, and species in the genus Peranemopsis to the genus Jenningsia. Key words: Euglenida, Protozoa, Chasmostoma nieuportense, Jenningsia diatomophaga, Jenningsia fusiforme n. comb., Jenningsia macrostoma n. comb., Jenningsia curvicauda n. comb., Jenningsia deflexum n. comb., Jenningsia furcatum n. comb., Jenningsia glabrum n. comb., Jenningsia granulifera n. comb., Jenningsia kupfferi n. comb., Jenningsia limax n. comb., Jenningsia macer n. comb., Jenningsia nigrum n. comb., Jenningsia sacculus n. comb. Introduction tioned in any subsequent reviews of euglenids (Huber- Pestalozzi, 1955; Leedale, 1967; Larsen and Patterson, Heterotrophic flagellates may be significant medita- 1991). -
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. -
Spatial and Temporal Distribution of Protozoa at Cueva De Los Riscos, Quere´Taro, Me´Xico
I. Sigala-Regalado, R. Maye´n-Estrada, and J. B. Morales-Malacara – Spatial and temporal distribution of protozoa at Cueva de Los Riscos, Quere´taro, Me´xico. Journal of Cave and Karst Studies, v. 73, no. 2, p. 55–62. DOI: 10.4311/jcks2009mb121 SPATIAL AND TEMPORAL DISTRIBUTION OF PROTOZOA AT CUEVA DE LOS RISCOS, QUERE´ TARO, ME´ XICO ITZEL SIGALA-REGALADO1,ROSAURA MAYE´ N-ESTRADA1,2, AND JUAN B. MORALES-MALACARA3,4 Abstract: Protozoa are important members of ecosystems, but protozoa that inhabit caves are poorly known worldwide. In this work, we present data on the record and distribution of thirteen protozoa species in four underground biotopes (water, soil, bat guano, and moss), at Cueva de Los Riscos. The samples were taken in six different months over more than a year. Protozoa species were ciliates (eight species), flagellates (three species), amoeboid (one species), and heliozoan (one species). Five of these species are reported for the first time inside cave systems anywhere, and an additional three species are new records for Mexican caves. Colpoda was the ciliate genera found in all cave zones sampled, and it inhabited the four biotopes together with Vorticella. The biotopes with the highest specific richness were the moss, sampled near the main cave entrance, and the temporary or permanent water bodies, with ten species each. The greatest number of species was observed in April 2006 (dry season). With the exception of water, all biotopes are studied for the first time. INTRODUCTION The protozoan trophozoite or cyst phase enters caves in water flow or infiltration through soil, in air currents, and A great extent of Mexican territory is formed by by troglophile fauna present in the cave (Golemansky and sedimentary rocks that permit the formation of caves, but Bonnet, 1994) and accidental or trogloxene organisms. -
Multi-Gene Phylogenetic Analysis of the Supergroup Excavata
MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN (Under the Direction of Mark A. Farmer) ABSTRACT The supergroup Excavata, one of six supergroups of eukaryotes, has been a controversial supergroup within the Eukaryotic Tree of Life. Excavata was originally based largely on morphological data and to date has not been well supported by molecular studies. The goals of this research were to test the monophyly of Excavata and to observe relationships among the nine subgroups of excavates included in this study. Several different types of phylogenetic analyses were performed on a data set consisting of sequences from nine reasonably conserved genes. Analyses of this data set recovered monophyly of Excavata with moderate to strong support. Topology tests rejected all but two topologies: one with a monophyletic Excavata and one with Excavata split into two major clades. Simple gap coding, which was performed on the ribosomal DNA alignments, was found to be more useful for species-level analyses than deeper relationships with the eukaryotes. INDEX WORDS: Excavata, excavates, monophyly, phylogenetic analysis, gap coding MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN B.S., Georgia Institute of Technology, 2002 A Thesis Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE ATHENS, GEORGIA 2009 © 2009 Christina Castlejohn All Rights Reserved MULTI-GENE PHYLOGENETIC ANALYSIS OF THE SUPERGROUP EXCAVATA By CHRISTINA CASTLEJOHN Major Professor: Mark A. Farmer Committee: James Leebens-Mack Joseph McHugh Electronic Version Approved: Maureen Grasso Dean of the Graduate School The University of Georgia August 2009 iv DEDICATION To my family, who have supported me in my journey v ACKNOWLEDGEMENTS I would like to thank Mark Farmer for helping me so much in my pursuit of higher education and my plans for the future. -
Investigating the Ecological Role of Cell Signaling in Free-Living Marine
AN ABSTRACT OF THE THESIS OF Aaron J. Hartz for the degree of Master of Science in Oceanography presented on May 26, 2010. Title: Investigating the Ecological Role of Cell Signaling in Free‐Living Marine Heterotrophic Protists. Abstract approved: Barry F. Sherr Phagotrophic protists are major consumers of microbial biomass in aquatic ecosystems. However, biochemical mechanisms underlying prey recognition and phagocytosis by protists are not well understood. We investigated the potential roles of cell signaling mechanisms in chemosensory response to prey, and in capture of prey cells, by a marine ciliate (Uronema sp.) and a heterotrophic dinoflagellate (Oxyrrhis marina). Inhibition of protein kinase signal transduction caused a decrease in both chemosensory response and predation. Inhibition of G protein coupled receptor signaling pathways significantly decreased chemosensory response but had no effect on prey ingestion. Inhibitor compounds did not appear to affect general cell health, but had a targeted effect. In addition, upon finding rhodopsin in protein extracts from the plasma membrane of O. marina, an investigation into the photosensory behavior of O. marina was made. This organism has a positive phototactic response to moderate levels of white light and a wavelength‐specific phototactic response. O. marina response to light was affected by culture conditions and feeding state. In the presence of blue light, phytoplankton emit red fluorescence; results indicate that in the presence of blue light, O. marina exhibited a positive phototactic response to a simulated “patch” of phytoplankton suggesting the use of the photoreceptor to detect the red phytoplankton fluorescence. These results support the idea that cell signaling pathways known in other eukaryotic organisms are involved in feeding behavior of free‐living protists.