A Practical Implementation of Large Transcriptomic Data Analysis to Resolve Cryptic Species Diversity Problems in Microbial Eukaryotes Yonas I
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Protistology Mitochondrial Genomes of Amoebozoa
Protistology 13 (4), 179–191 (2019) Protistology Mitochondrial genomes of Amoebozoa Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova1,2, Anna Glotova1,2 and Anna Maria Fiore-Donno3 1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia 2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia 3 University of Cologne, Institute of Zoology, Terrestrial Ecology, 50674 Cologne, Germany | Submitted November 28, 2019 | Accepted December 10, 2019 | Summary In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial -
Differential Gene Expression Analysis and Cytological Evidence Reveal a Sexual Stage of an Amoeba with Multiparental Cellular and Nuclear Fusion
PLOS ONE RESEARCH ARTICLE Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion ☯ ☯ Yonas I. TekleID *, Fang Wang , Alireza Heidari, Alanna Johnson Stewart Department of Biology, Spelman College, Atlanta, Georgia, United States of America a1111111111 ☯ These authors contributed equally to this work. a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary OPEN ACCESS for sexual reproduction. However, the mechanism of sexual development in a majority of Citation: Tekle YI, Wang F, Heidari A, Stewart AJ microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in (2020) Differential gene expression analysis and studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cytological evidence reveal a sexual stage of an cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investi- amoeba with multiparental cellular and nuclear fusion. PLoS ONE 15(11): e0235725. https://doi. gate sexual development using stage-specific Differential Gene Expression (DGE) and org/10.1371/journal.pone.0235725 cytological analyses. Both DGE and cytological results showed that most of the meiosis and Editor: Arthur J. Lustig, Tulane University Health sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Sciences Center, UNITED STATES Relative gene ontology (GO) category representations in unfused and fused cells revealed Received: June 19, 2020 a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. -
A Revised Classification of Naked Lobose Amoebae (Amoebozoa
Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility. -
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). -
Vita: OR Anderson
CURRICULUM VITA O. Roger Anderson [Updated May 2020] BIRTH DATE: August 4, 1937 OCCUPATION: Microbial Physiological Ecologist, Biologist, and Educator PROFESSIONAL RANK: Professor of Natural Sciences, Columbia University T. C., 1964-present Teachers College ; Department Chairman, 1974-1980, 1993-1996, 2000-2017 Senior Research Scientist (Adj.), Biology, 1967-present Lamont-Doherty Earth Observatory of Columbia University Faculty Member at Large, Columbia University Graduate School of Arts and Sciences. 1993-present DEGREES: Bachelor of Arts (Botany) Washington University, St. Louis 1959 Master of Arts (Biological Education) Washington University 1961 Doctorate (Biology and Education) Washington University 1964 PROFESSIONAL EXPERIENCE (TEACHING): 1963-64 Washington University, St. Louis 1964-67 Assistant Professor of Natural Sciences Columbia University, Teachers College 1968-70 Associate Professor of Natural Sciences Columbia University, Teachers College 1971- Professor of Natural Sciences Columbia University, Teachers College 1992-1993 College Research Coordinator, Teachers College. 1993-1996 Associate Director, Division of Instruction, T. C. OFFICES IN NATIONAL AND INTERNATIONAL ORGANIZATIONS: 1976 President, National Association for Res. Science Teaching (International) 1993-95 President, Columbia University Chapter Sigma Xi Honorary Scientific Society (National) 1995 President, International Society of Protistology (International) ---------------------------------------------------------------------------------------------------- -
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. -
THE THECAMOEBIAN BIBLIOGRAPHY 2Nd Edition
Palaeontologia Electronica http://palaeo-electronica.org Preamble to the 2nd Edition. Since the publication of the first edition we have collected about 1,000 new titles which are inserted in the second edition. All the remarks and caveats in the Introduction are valid for both editions. The first edition of this document was published in 1999. THE THECAMOEBIAN BIBLIOGRAPHY 2nd Edition F.S. Medioli, L. Bonnet, David B. Scott, and Barbara Elizabeth Medioli ABSTRACT The literature on thecamoebians can be rather confusing, partly because it has been published in many different languages, but mainly because these Rhizopoda have been the subject of study for a wide array of researchers with very different inter- ests. Not only has this resulted in fragmentation of the literature due to research results being published in journals specializing in different fields, but inevitably has also resulted in development of a chaotic terminology and nomenclature. For example there is even confusion as to what to call the group, as terms such as "rhizopods," "testate amoebae," and "arcellaceans" have all been used by various authors as synonyms of "Thecamoebians." Even more confusing is the nomenclature of the described the- camoebian species. Lack of access to the literature and limited interchange between the various research groups has generated many synonyms. Although only a first step this fairly complete bibliography on thecamoebians has been compiled to assist researchers become more aware of the available literature. F.S. Medioli, David B. Scott. Dalhousie University, Department of Earth Sciences, Halifax, Nova Scotia, B3H 3J5, Canada. [email protected]. [email protected]. -
Freshwater Silica-Scaled Heterotrophic Protista: Heliozoa, Thaumatomonad Flagellates, Amoebae, and Bicosoecids, from the Lake Itasca Region, Minnesota
JOURNAL OF THE MINNESOTA ACADEMY OF SCIENCE VOL. 78 NO. 2 (2015) FRESHWATER SILICA-SCALED HETEROTROPHIC PROTISTA: HELIOZOA, THAUMATOMONAD FLAGELLATES, AMOEBAE, AND BICOSOECIDS, FROM THE LAKE ITASCA REGION, MINNESOTA Daniel E. Wujek Central Michigan University, Mt. Pleasant, MI Forty-nine plankton samples were collected from the Lake Itasca Region, Minnesota over a period sporadically covering the summers of 1980, 1981 and 1987. A total of 22 freshwater heterotrophic siliceous-scaled species were observed: 18 heliozoa, two thaumatomonad flagellates, one bicosoecid, and one testate amoeba. Scale identifications were based on transmission electron microscopy. New records for North America include two heliozoans and one thaumatomonad flagellate. Five heliozoa taxa and one thaumatomonad flagellate are new records for the U.S. Wujek DE. Freshwater silica-scaled heterotrophic protista: heliozoa, thaumatomonad flagellates, amoebae, and bicosoecids, from the Lake Itasca Region, Minnesota. Minnesota Academy of Science Journal. 2015; 78(2):1-14. Keywords: bicosoecids, heliozoa, protista, testate amoeba, thaumatomonad flagellates Daniel E Wujek, Department of Biology, Central microscopy (EM) usually is necessary to distinguish Michigan University, Mt. Pleasant, MI 48859, e- sufficient morphology for species identification in the mail: [email protected]. scaled chrysophyte groups3 and now have become the This study was in part funded by a grant from the tool for other scaled protists. CMU FRCE committee. North American heterotrophic protist studies -
Description of Cochliopodium Massiliensis Sp. Nov., Isolated in Bronchoalveolar Lavage of a Tunisian Patient with Pneumonia
Hanene Saadi, Gabrielle Boussay, Maryse Loinard, Akila Boussaid, Mondher Boughalmi 010 International Journal of Latest Trends in Engineering and Technology Vol.(13)Issue(3), pp.010-015 DOI: http://dx.doi.org/10.21172/1.133.02 e-ISSN:2278-621X DESCRIPTION OF COCHLIOPODIUM MASSILIENSIS SP. NOV., ISOLATED IN BRONCHOALVEOLAR LAVAGE OF A TUNISIAN PATIENT WITH PNEUMONIA. Hanene Saadi1, Gabrielle Boussay2, Maryse Loinard3, Akila Boussaid4, Mondher Boughalmi5 Abstract- In this work, we describe the isolation of Cochliopodium massiliensis sp nov in a bronchoalveolar lavage from a patient with pneumonia. It is the first international isolate of this genus of amoeba in a human sample but also the first case described during this pathology. This new species is the smallest of the Cochliopodium species already described. Cochliopodium massiliensis sp nov is described on the basis of morphological observations in light microscopy, ultrastructure by TEM microscopy and molecular genetic evidence of SSU rDNA. Cochliopodium massiliensis n. sp (length ~ 16μm) is characterized by the presence on the surface of complex structures called Scale. Containing a apical funnel shaped collar (~560 nm), dorsal and ventral bases plate of the Scale (with radius ~ 420 nm). Based on morphological and molecular genetic data of SSU-DNA gene, we describe our isolate as a new species, the first isolate of this genus from a human biological sample, and the first case described during pneumonia. Key words: Cochliopodiidae, Cochliopoduim, ultrastructure, comparative morphology, phylogeny, SSU-rDNA, taxonomy. 1. INTRODUCTION Amoebae are micro-organisms that have a complex spatial and temporal distribution in all ecological niches, from freshwater (Acanthamoeba sp) to the most extreme environments (Halophilic Heterolobosean). -
Cochliopodium Minus, a Scale-Bearing Amoeba Isolated from Organs of Perch Perca Fluviatilis
DISEASES OF AQUATIC ORGANISMS Published November 30 Dis Aquat Ory Cochliopodium minus, a scale-bearing amoeba isolated from organs of perch Perca fluviatilis I. Dykova*, J. Lom, B. MachaEkova Institute of Parasitology, Academy of Sciences of the Czech Republic, CZ-370 05 (reske Budejovice, Czech Republic ABSTRACT: A scale-bearing amoeba isolated from gills and other organs of perch Perca fluviatilis Lin- naeus, 1758 was identified as Cochliopodium minus Page, 1976. This assignment was suggested by light microscopy and confirmed by ultrastructural study of both the strain isolated from perch and the environmental strain of C. minus (CCAP 1537/1A) serving as a control. This has been the first electron- microscopic definition of C. minus and, in addition, the first identification of an amoeba with a theca- like cover found to infect fish. The ability of the fish strain of C. minus to colonize gills and also internal body organs was proved experimentally. KEY WORDS: Free living amoebae . Cochliopodium minus . Ultrastructure . Systemic infection of fish INTRODUCTION also examined in C. bilimbosum by Sadakane et al. (1996). The most important outbreaks of amoebic gill dis- The goals of the present st.udy were to report the iso- eases (AGD)resulting in mortalities have been recorded lation of a Cochliopodium sp. from the gills and other in salmonids. Among the agents, Paramoeba spp, evi- organs of perch Perca fluviatilis Linnaeus, 1758, and to dently play the most important role in marine cultures, present its ultrastructural features. while amoebae of the families Cochliopodidae and Thecamoebidae have been recorded as agents of severe gill lesions in freshwater farmed Oncorhynchus MATERIALS AND METHODS mykiss (Sawyer et al. -
Sarcodina: Amoebae
NOAA Technical Report NMFS Circular 419 Marine Flora and Fauna of the Northeastern United States. Protozoa: Sarcodina: Amoebae Eugene C. Bovee and Thomas K. Sawyer January 1979 U.S. DEPARTMENT OF COMMERCE Juanita M. Kreps, Secretary National Oceanic and Atmospheric Administration Richard A. Frank, Administrator Terry L. Leitzell, Assistant Administrator for Fisheries National Marine Fisheries Service For S;le!:;y the· Superintendent of -DOeum~;:':ts-:-U.S. Government" Printi;:;-g -offict;' Washington, D.C. 20402 Stock No. 003-017-00433-3 FOREWORD This issue of the "Circulars" is part of a subseries entitled "Marine Flora and Fauna of the Northeastern Unit.ed States." This subseries will consist of original, illustrated, modern manuals on the identification, classification, and general biology of the estuarine and coastal marine plants and animals of the northeastern United States. Manuals will be published at irregular intervals on as many taxa of the region as there afe specialists available to collaborate in their preparation. The manuals are an outgrowth of the widely used "Keys to Marine Invertebrates of the Woods Hole Region," edited by R. I. Smith, published in 1964, and produced under the auspices of the Systematics-Ecology Program, Marine Biological Laboratory, Woods Hole, Mass. Instead of revising the "Woods Hole Keys," the staff of the Systematics-Ecology Program decided to ex pand the geographic coverage and bathymetric range and produce the keys in an entirely new set of expanded publications. The "Marine Flora and Fauna of the ~ortheastern United States" is being prepared in collaboration with systematic specialists in the United States and abroad. Each manual will be based primarily on recent and ongoing revisionary systematic research and a fresh examination of the plants and animals. -
Frozen Zoo: a Collection of Permafrost Samples Containing Viable Protists and Their Viruses
Biodiversity Data Journal 8: e51586 doi: 10.3897/BDJ.8.e51586 Data Paper Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses Stas Malavin‡, Lyubov Shmakova‡, Jean-Michel Claverie§, Elizaveta Rivkina‡ ‡ Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia § Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Marseille, France Corresponding author: Stas Malavin ([email protected]) Academic editor: Anna Maria Fiore-Donno Received: 28 Feb 2020 | Accepted: 03 Jul 2020 | Published: 10 Jul 2020 Citation: Malavin S, Shmakova L, Claverie J-M, Rivkina E (2020) Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses. Biodiversity Data Journal 8: e51586. https://doi.org/10.3897/BDJ.8.e51586 Abstract Background Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to 1000 metres depth. Due to constant subzero temperatures, permafrost represents a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several protist strains and two giant protist viruses isolated from permafrost cores have been already described. New information In this paper, we describe a collection of 35 amoeboid protist strains isolated from the samples of Holocene and Pleistocene permanently frozen sediments. These samples are stored at −18°C in the Soil Cryology Lab, Pushchino, Russia and may be used for further studies and isolation attempts.