Defining Planktonic Protist Functional Groups on Mechanisms for Energy
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Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed. -
Destabilization, Stabilization, and Multiple Attractors in Saturated Mixotrophic Environments
Downloaded from orbit.dtu.dk on: Sep 27, 2021 Destabilization, stabilization, and multiple attractors in saturated mixotrophic environments Lindstrom, Torsten; Cheng, Yuanji; Chakraborty, Subhendu Published in: SIAM Journal on Applied Mathematics Link to article, DOI: 10.1137/19M1294186 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Lindstrom, T., Cheng, Y., & Chakraborty, S. (2020). Destabilization, stabilization, and multiple attractors in saturated mixotrophic environments. SIAM Journal on Applied Mathematics, 80(6), 2338-2364. https://doi.org/10.1137/19M1294186 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. SIAM J. APPL.MATH. © 2020 Society for Industrial and Applied Mathematics Vol. 80, No. 6, pp. 2338{2364 DESTABILIZATION, STABILIZATION, AND MULTIPLE ATTRACTORS IN SATURATED MIXOTROPHIC ENVIRONMENTS\ast \" y z x TORSTEN LINDSTROM , YUANJI CHENG , AND SUBHENDU CHAKRABORTY Abstract. The ability of mixotrophs to combine phototrophy and phagotrophy is now well recognized and found to have important implications for ecosystem dynamics. -
28-Protistsf20r.Ppt [Compatibility Mode]
9/3/20 Ch 28: The Protists (a.k.a. Protoctists) (meet these in more detail in your book and lab) 1 Protists invent: eukaryotic cells size complexity Remember: 1°(primary) endosymbiosis? -> mitochondrion -> chloroplast genome unicellular -> multicellular 2 1 9/3/20 For chloroplasts 2° (secondary) happened (more complicated) {3°(tertiary) happened too} 3 4 Eukaryotic “supergroups” (SG; between K and P) 4 2 9/3/20 Protists invent sex: meiosis and fertilization -> 3 Life Cycles/Histories (Fig 13.6) Spores and some protists (Humans do this one) 5 “Algae” Group PS Pigments Euglenoids chl a & b (& carotenoids) Dinoflagellates chl a & c (usually) (& carotenoids) Diatoms chl a & c (& carotenoids) Xanthophytes chl a & c (& carotenoids) Chrysophytes chl a & c (& carotenoids) Coccolithophorids chl a & c (& carotenoids) Browns chl a & c (& carotenoids) Reds chl a, phycobilins (& carotenoids) Greens chl a & b (& carotenoids) (more groups exist) 6 3 9/3/20 Name word roots (indicate nutrition) “algae” (-phyt-) protozoa (no consistent word ending) “fungal-like” (-myc-) Ecological terms plankton phytoplankton zooplankton 7 SG: Excavata/Excavates “excavated” feeding groove some have reduced mitochondria (e.g.: mitosomes, hydrogenosomes) 8 4 9/3/20 SG: Excavata O: Diplomonads: †Giardia Cl: Parabasalids: Trichonympha (bk only) †Trichomonas P: Euglenophyta/zoa C: Kinetoplastids = trypanosomes/hemoflagellates: †Trypanosoma C: Euglenids: Euglena 9 SG: “SAR” clade: Clade Alveolates cell membrane 10 5 9/3/20 SG: “SAR” clade: Clade Alveolates P: Dinoflagellata/Pyrrophyta: -
The Macronuclear Genome of Stentor Coeruleus Reveals Tiny Introns in a Giant Cell
University of Pennsylvania ScholarlyCommons Departmental Papers (Biology) Department of Biology 2-20-2017 The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Mark M. Slabodnick University of California, San Francisco J. G. Ruby University of California, San Francisco Sarah B. Reiff University of California, San Francisco Estienne C. Swart University of Bern Sager J. Gosai University of Pennsylvania See next page for additional authors Follow this and additional works at: https://repository.upenn.edu/biology_papers Recommended Citation Slabodnick, M. M., Ruby, J. G., Reiff, S. B., Swart, E. C., Gosai, S. J., Prabakaran, S., Witkowska, E., Larue, G. E., Gregory, B. D., Nowacki, M., Derisi, J., Roy, S. W., Marshall, W. F., & Sood, P. (2017). The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Current Biology, 27 (4), 569-575. http://dx.doi.org/10.1016/j.cub.2016.12.057 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/biology_papers/49 For more information, please contact [email protected]. The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell Abstract The giant, single-celled organism Stentor coeruleus has a long history as a model system for studying pattern formation and regeneration in single cells. Stentor [1, 2] is a heterotrichous ciliate distantly related to familiar ciliate models, such as Tetrahymena or Paramecium. The primary distinguishing feature of Stentor is its incredible size: a single cell is 1 mm long. Early developmental biologists, including T.H. Morgan [3], were attracted to the system because of its regenerative abilities—if large portions of a cell are surgically removed, the remnant reorganizes into a normal-looking but smaller cell with correct proportionality [2, 3]. -
Bioenergetics of Mixotrophic Metabolisms: a Theoretical Analysis
Bioenergetics of mixotrophic metabolisms: A theoretical analysis by Stephanie Slowinski A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Earth Sciences (Water) Waterloo, Ontario, Canada, 2019 © Stephanie Slowinski 2019 Author’s Declaration This thesis consists of material all of which I authored or co-authored: see Statement of Contributions included in the thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Statement of Contributions This thesis consists of two co-authored chapters. I contributed to the study design and execution in chapters 2 and 3. Christina M. Smeaton (CMS) and Philippe Van Cappellen (PVC) provided guidance during the study design and analysis. I co-authored both of these chapters with CMS and PVC. iii Abstract Many biogeochemical reactions controlling surface water and groundwater quality, as well as greenhouse gas emissions and carbon turnover rates, are catalyzed by microorganisms. Representing the thermodynamic (or bioenergetic) constraints on the reduction-oxidation reactions carried out by microorganisms in the subsurface is essential to understand and predict how microbial activity affects the environmental fate and transport of chemicals. While organic compounds are often considered to be the primary electron donors (EDs) in the subsurface, many microorganisms use inorganic EDs and are capable of autotrophic carbon fixation. Furthermore, many microorganisms and communities are likely capable of mixotrophy, switching between heterotrophic and autotrophic metabolisms according to the environmental conditions and energetic substrates available to them. -
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. -
There Is Not a Latin Root Word Clear Your Desk Protist Quiz Grade Quiz
There is not a Latin Root Word Clear your desk Protist Quiz Grade Quiz Malaria Fever Wars Classification Kingdom Protista contains THREE main groups of organisms: 1. Protozoa: “animal-like protists” 2. Algae: “plant-like protists” 3. Slime & Water Molds: “fungus-like protists” Basics of Protozoa Unicellular Eukaryotic unlike bacteria 65, 000 different species Heterotrophic Free-living (move in aquatic environments) or Parasitic Habitats include oceans, rivers, ponds, soil, and other organisms. Protozoa Reproduction ALL protozoa can use asexual reproduction through binary fission or multiple fission FEW protozoa reproduce sexually through conjugation. Adaptation Special Protozoa Adaptations Eyespot: detects changes in the quantity/ quality of light, and physical/chemical changes in their environment Cyst: hardened external covering that protects protozoa in extreme environments. Basics of Algae: “Plant-like” protists. MOST unicellular; SOME multicellular. Make food by photosynthesis (“autotrophic prostists”). Were classified as plants, BUT… – Lack tissue differentiation- NO roots, stems, leaves, etc. – Reproduce differently Most algal cells have pyrenoids (organelles that make and store starch) Can use asexual or sexual reproduction. Algae Structure: Thallus: body portion; usually haploid Body Structure: 1) unicellular: single-celled; aquatic (Ex.phytoplankton, Chlamydomonas) 2) colonial: groups of coordinated cells; “division of labor” (Ex. Volvox) 3) filamentous: rod-shaped thallus; some anchor to ocean bottom (Ex. Spyrogyra) 4) multicellular: large, complex, leaflike thallus (Ex. Macrocystis- giant kelp) Basics of Fungus-like Protists: Slime Molds: Water Molds: Once classified as fungi Fungus-like; composed of Found in damp soil, branching filaments rotting logs, and other Commonly freshwater; decaying matter. some in soil; some Some white, most yellow parasites. -
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 -
Wrc Research Report No. 131 Effects of Feedlot Runoff
WRC RESEARCH REPORT NO. 131 EFFECTS OF FEEDLOT RUNOFF ON FREE-LIVING AQUATIC CILIATED PROTOZOA BY Kenneth S. Todd, Jr. College of Veterinary Medicine Department of Veterinary Pathology and Hygiene University of Illinois Urbana, Illinois 61801 FINAL REPORT PROJECT NO. A-074-ILL This project was partially supported by the U. S. ~epartmentof the Interior in accordance with the Water Resources Research Act of 1964, P .L. 88-379, Agreement No. 14-31-0001-7030. UNIVERSITY OF ILLINOIS WATER RESOURCES CENTER 2535 Hydrosystems Laboratory Urbana, Illinois 61801 AUGUST 1977 ABSTRACT Water samples and free-living and sessite ciliated protozoa were col- lected at various distances above and below a stream that received runoff from a feedlot. No correlation was found between the species of protozoa recovered, water chemistry, location in the stream, or time of collection. Kenneth S. Todd, Jr'. EFFECTS OF FEEDLOT RUNOFF ON FREE-LIVING AQUATIC CILIATED PROTOZOA Final Report Project A-074-ILL, Office of Water Resources Research, Department of the Interior, August 1977, Washington, D.C., 13 p. KEYWORDS--*ciliated protozoa/feed lots runoff/*water pollution/water chemistry/Illinois/surface water INTRODUCTION The current trend for feeding livestock in the United States is toward large confinement types of operation. Most of these large commercial feedlots have some means of manure disposal and programs to prevent runoff from feed- lots from reaching streams. However, there are still large numbers of smaller feedlots, many of which do not have adequate facilities for disposal of manure or preventing runoff from reaching waterways. The production of wastes by domestic animals was often not considered in the past, but management of wastes is currently one of the largest problems facing the livestock industry. -
Aerobic Respiration
Life is based on redox • All energy generation in biological systems is due to redox (reduction-oxidation) reactions Aerobic Respiration: + - C6H12O6 + 6 H2O ==> 6 CO2 + 24 H +24 e oxidation electron donor (aka energy source) + - (O2+ 4H + 4e ==> 2H2O) x6 reduction electron acceptor --------------------------------------- C6H12O6 + 6 O2 ==> 6 CO2 + 6 H2O overall reaction (24 electrons) Types of bacterial metabolisms • While eukaryotes only reduce O2 and oxidize organic compounds, prokaryotes can use a variety of electron donors and acceptors, organic and inorganic. - • Aerobic respiration: e acceptor is O2 - • Anaerobic respiration: e acceptor is not O2 • Fermentation: e- donor and acceptor are organic molecules • Chemolithotrophy: e- donor and acceptor are inorganic molecules • Phototrophy: e- donor is light and e- acceptor is either organic or inorganic all microorganisms energy source? chemical light chemotroph phototroph carbon source? carbon source? organic organic CO CO compound 2 compound 2 chemoheterotroph chemoautotroph photoheterotroph photoautotroph e- acceptor? Nitrifying and sulfur- use H O to reduce CO ? oxidizing bacteria 2 2 green non-sulfur and O Other than O 2 2 purple non-sulfur bacteria anoxygenic oxygenic photosynthesis: photosynthesis: green sulfur and most bacteria Organic Inorganic cyanobacteria compound compound purple sulfur bacteria fermentative organism anaerobic respiration: nitrate, sulfate, Fe(III) Aerobic or anaerobic respiration Chemolithotrophy Important molecules Redox Electron Carrier: for example the -
Medical Parasitology
MEDICAL PARASITOLOGY Anna B. Semerjyan Marina G. Susanyan Yerevan State Medical University Yerevan 2020 1 Chapter 15 Medical Parasitology. General understandings Parasitology is the study of parasites, their hosts, and the relationship between them. Medical Parasitology focuses on parasites which cause diseases in humans. Awareness and understanding about medically important parasites is necessary for proper diagnosis, prevention and treatment of parasitic diseases. The most important element in diagnosing a parasitic infection is the knowledge of the biology, or life cycle, of the parasites. Medical parasitology traditionally has included the study of three major groups of animals: 1. Parasitic protozoa (protists). 2. Parasitic worms (helminthes). 3. Arthropods that directly cause disease or act as transmitters of various pathogens. Parasitism is a form of association between organisms of different species known as symbiosis. Symbiosis means literally “living together”. Symbiosis can be between any plant, animal, or protist that is intimately associated with another organism of a different species. The most common types of symbiosis are commensalism, mutualism and parasitism. 1. Commensalism involves one-way benefit, but no harm is exerted in either direction. For example, mouth amoeba Entamoeba gingivalis, uses human for habitat (mouth cavity) and for food source without harming the host organism. 2. Mutualism is a highly interdependent association, in which both partners benefit from the relationship: two-way (mutual) benefit and no harm. Each member depends upon the other. For example, in humans’ large intestine the bacterium Escherichia coli produces the complex of vitamin B and suppresses pathogenic fungi, bacteria, while sheltering and getting nutrients in the intestine. 3. -
PROTISTAS MARINOS Viviana A
PROTISTAS MARINOS Viviana A. Alder INTRODUCCIÓN plantas y animales. Según este esquema básico, a las plantas les correspondían las características de En 1673, el editor de Philosophical Transac- ser organismos sésiles con pigmentos fotosinté- tions of the Royal Society of London recibió una ticos para la síntesis de las sustancias esenciales carta del anatomista Regnier de Graaf informan- para su metabolismo a partir de sustancias inor- do que un comerciante holandés, Antonie van gánicas (nutrición autótrofa), y de poseer células Leeuwenhoek, había “diseñado microscopios rodeadas por paredes de celulosa. En oposición muy superiores a aquéllos que hemos visto has- a las plantas, les correspondía a los animales los ta ahora”. Van Leeuwenhoek vendía lana, algo- atributos de tener motilidad activa y de carecer dón y otros materiales textiles, y se había visto tanto de pigmentos fotosintéticos (debiendo por en la necesidad de mejorar las lentes de aumento lo tanto procurarse su alimento a partir de sustan- que comúnmente usaba para contar el número cias orgánicas sintetizadas por otros organismos) de hebras y evaluar la calidad de fibras y tejidos. como de paredes celulósicas en sus células. Así fue que construyó su primer microscopio de Es a partir de los estudios de Georg Gol- lente única: simple, pequeño, pero con un poder dfuss (1782-1848) que estos diminutos organis- de magnificación de hasta 300 aumentos (¡diez mos, invisibles a ojo desnudo, comienzan a ser veces más que sus precursores!). Este magnífico clasificados como plantas primarias