Comparative Analysis of Various Media and Food Source on Culturing of the Eukaryotic Microbe Blepharisma
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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. -
Novel Interactions Between Phytoplankton and Microzooplankton: Their Influence on the Coupling Between Growth and Grazing Rates in the Sea
Hydrobiologia 480: 41–54, 2002. 41 C.E. Lee, S. Strom & J. Yen (eds), Progress in Zooplankton Biology: Ecology, Systematics, and Behavior. © 2002 Kluwer Academic Publishers. Printed in the Netherlands. Novel interactions between phytoplankton and microzooplankton: their influence on the coupling between growth and grazing rates in the sea Suzanne Strom Shannon Point Marine Center, Western Washington University, 1900 Shannon Point Rd., Anacortes, WA 98221, U.S.A. Tel: 360-293-2188. E-mail: [email protected] Key words: phytoplankton, microzooplankton, grazing, stability, behavior, evolution Abstract Understanding the processes that regulate phytoplankton biomass and growth rate remains one of the central issues for biological oceanography. While the role of resources in phytoplankton regulation (‘bottom up’ control) has been explored extensively, the role of grazing (‘top down’ control) is less well understood. This paper seeks to apply the approach pioneered by Frost and others, i.e. exploring consequences of individual grazer behavior for whole ecosystems, to questions about microzooplankton–phytoplankton interactions. Given the diversity and paucity of phytoplankton prey in much of the sea, there should be strong pressure for microzooplankton, the primary grazers of most phytoplankton, to evolve strategies that maximize prey encounter and utilization while allowing for survival in times of scarcity. These strategies include higher grazing rates on faster-growing phytoplankton cells, the direct use of light for enhancement of protist digestion rates, nutritional plasticity, rapid population growth combined with formation of resting stages, and defenses against predatory zooplankton. Most of these phenomena should increase community-level coupling (i.e. the degree of instantaneous and time-dependent similarity) between rates of phytoplankton growth and microzooplankton grazing, tending to stabilize planktonic ecosystems. -
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]. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
(Alveolata) As Inferred from Hsp90 and Actin Phylogenies1
J. Phycol. 40, 341–350 (2004) r 2004 Phycological Society of America DOI: 10.1111/j.1529-8817.2004.03129.x EARLY EVOLUTIONARY HISTORY OF DINOFLAGELLATES AND APICOMPLEXANS (ALVEOLATA) AS INFERRED FROM HSP90 AND ACTIN PHYLOGENIES1 Brian S. Leander2 and Patrick J. Keeling Canadian Institute for Advanced Research, Program in Evolutionary Biology, Departments of Botany and Zoology, University of British Columbia, Vancouver, British Columbia, Canada Three extremely diverse groups of unicellular The Alveolata is one of the most biologically diverse eukaryotes comprise the Alveolata: ciliates, dino- supergroups of eukaryotic microorganisms, consisting flagellates, and apicomplexans. The vast phenotypic of ciliates, dinoflagellates, apicomplexans, and several distances between the three groups along with the minor lineages. Although molecular phylogenies un- enigmatic distribution of plastids and the economic equivocally support the monophyly of alveolates, and medical importance of several representative members of the group share only a few derived species (e.g. Plasmodium, Toxoplasma, Perkinsus, and morphological features, such as distinctive patterns of Pfiesteria) have stimulated a great deal of specula- cortical vesicles (syn. alveoli or amphiesmal vesicles) tion on the early evolutionary history of alveolates. subtending the plasma membrane and presumptive A robust phylogenetic framework for alveolate pinocytotic structures, called ‘‘micropores’’ (Cavalier- diversity will provide the context necessary for Smith 1993, Siddall et al. 1997, Patterson -
Fine Structure of Division in Ciliate Protozoa I
FINE STRUCTURE OF DIVISION IN CILIATE PROTOZOA I. Micronuclear Mitosis in Blepharisma R. A. JENKINS From the Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50010. The author's present address is the Department of Zoology and Physiology, University of Wy- oming, Laramie, Wyoming 82070 ABSTRACT The mitotic, micronuclear division of the heterotrichous genus Blepharisma has been studied by electron microscopy. Dividing ciliates were selected from clone-derived mass cultures and fixed for electron microscopy by exposure to the vapor of 2 % osmium tetroxide; individual Blepharisma were encapsulated and sectioned. Distinctive features of the mitosis are the pres- ence of an intact nuclear envelope during the entire process and the absence of centrioles at the polar ends of the micronuclear figures. Spindle microtubules (SMT) first appear in ad- vance of chromosome alignment, become more numerous and precisely aligned by meta- phase, lengthen greatly in anaphase, and persist through telophase. Distinct chromosomal and continuous SMT are present. At telophase, daughter nuclei are separated by a spindle elongation of more than 40 u, and a new nuclear envelope is formed in close apposition to the chromatin mass of each daughter nucleus and excludes the great amount of spindle material formed during division. The original nuclear envelope which has remained struc- turally intact then becomes discontinuous and releases the newly formed nucleus into the cytoplasm. The micronuclear envelope seems to lack the conspicuous pores that are typical of nuclear envelopes. The morphology, size, formation, and function of SMT and the nature of micronuclear division are discussed. INTRODUCTION To date electron microscopy of protozoan nuclei includes almost no description of micronuclei has resulted in the description of numerous and and by the recent suggestion that a true mitosis diverse structures which are not always reconcil- does not occur in ciliate micronuclei (9). -
Protozoa and Oxygen
Acta Protozool. (2014) 53: 3–12 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.13.0020.1117 Protozoologica Special issue: Marine Heterotrophic Protists Guest editors: John R. Dolan and David J. S. Montagnes Review paper Protozoa and Oxygen Tom FENCHEL Marine Biological Laboratory, University of Copenhagen, Denmark Abstract. Aerobic protozoa can maintain fully aerobic metabolic rates even at very low O2-tensions; this is related to their small sizes. Many – or perhaps all – protozoa show particular preferences for a given range of O2-tensions. The reasons for this and the role for their distribution in nature are discussed and examples of protozoan biota in O2-gradients in aquatic systems are presented. Facultative anaerobes capable of both aerobic and anaerobic growth are probably common within several protozoan taxa. It is concluded that further progress in this area is contingent on physiological studies of phenotypes. Key words: Protozoa, chemosensory behavior, oxygen, oxygen toxicity, microaerobic protozoa, facultative anaerobes, microaerobic and anaerobic habitats. INTRODUCTION low molecular weight organics and in some cases H2 as metabolic end products. Some ciliates and foraminifera use nitrate as a terminal electron acceptor in a respira- Increasing evidence suggests that the last common tory process (for a review on anaerobic protozoa, see ancestor of extant eukaryotes was mitochondriate and Fenchel 2011). had an aerobic energy metabolism. While representa- The great majority of protozoan species, however, tives of different protist taxa have secondarily adapted depend on aerobic energy metabolism. Among pro- to an anaerobic life style, all known protists possess ei- tists with an aerobic metabolism many – or perhaps ther mitochondria capable of oxidative phosphorylation all – show preferences for particular levels of oxygen or – in anaerobic species – have modified mitochon- tension below atmospheric saturation. -
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. -
A Preliminary Survey on the Planktonic Biota in a Hypersaline Pond of Messolonghi Saltworks (W
diversity Article A Preliminary Survey on the Planktonic Biota in a Hypersaline Pond of Messolonghi Saltworks (W. Greece) George N. Hotos Plankton Culture Laboratory, Department of Animal Production, Fisheries & Aquaculture, University of Patras, 30200 Messolonghi, Greece; [email protected] Abstract: During a survey in 2015, an impressive assemblage of organisms was found in a hypersaline pond of the Messolonghi saltworks. The salinity ranged between 50 and 180 ppt, and the organisms that were found fell into the categories of Cyanobacteria (17 species), Chlorophytes (4 species), Diatoms (23 species), Dinoflagellates (1 species), Protozoa (40 species), Rotifers (8 species), Copepods (1 species), Artemia sp., one nematode and Alternaria sp. (Fungi). Fabrea salina was the most prominent protist among all samples and salinities. This ciliate has the potential to be a live food candidate for marine fish larvae. Asteromonas gracilis proved to be a sturdy microalga, performing well in a broad spectrum of culture salinities. Most of the specimens were identified to the genus level only. Based on their morphology, as there are no relevant records in Greece, there is a possibility for some to be either new species or strikingly different strains of certain species recorded elsewhere. Keywords: protists; cyanobacteria; rotifers; crustacea; hypersaline conditions; Messolonghi saltworks 1. Introduction Citation: Hotos, G.N. A Preliminary It is well known that saltwork waters support high algal densities due to the abun- Survey on the Planktonic Biota in a dance of nutrients concentrated by evaporation [1–3]. Apart from the fact that such Hypersaline Pond of Messolonghi ecosystems are of paramount ecological value, they are also a potential source for tolerant Saltworks (W. -
PDF Proof: Mol. Biol. Evol. 14 15 16 17 18 19 20 21 22 23 24 25 26 27 FIG
Page 1 of 61 Molecular Biology and Evolution 1 2 3 Submission intended as an Article for the section Resources of MBE 4 5 6 PhyloToL: A taxon/gene rich phylogenomic pipeline to explore genome evolution of 7 8 diverse eukaryotes 9 10 11 Cerón-Romero M. A a,b, Maurer-Alcalá, X. X. a,b,d, Grattepanche, J-D. a, e, Yan, Y. a, Fonseca, M. 12 c a,b. 13 M. , Katz, L. PDFA Proof: Mol. Biol. Evol. 14 15 16 a Department of Biological Sciences, Smith College, Northampton, Massachusetts, USA. 17 b Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, 18 19 Amherst, Massachusetts, USA. 20 c 21 CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of 22 Porto, Porto, Portugal. 23 24 d Current address: Institute of Cell Biology, University of Bern, Bern, Switzerland. 25 e Current address: Biology Department, Temple University, Philadelphia, Pennsylvania, USA. 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 ScholarOne, 375 Greenbrier Drive, Charlottesville, VA, 22901 Support: (434) 964-4100 Molecular Biology and Evolution Page 2 of 61 1 2 3 ABSTRACT 4 5 Estimating multiple sequence alignments (MSAs) and inferring phylogenies are essential for 6 many aspects of comparative biology. Yet, many bioinformatics tools for such analyses have 7 8 focused on specific clades, with greatest attention paid to plants, animals and fungi. The rapid 9 10 increase of high-throughput sequencing (HTS) data from diverse lineages now provides 11 opportunities to estimate evolutionary relationships and gene family evolution across the 12 13 eukaryotic treePDF of life. -
Microscope Worksheet Activity 1
Name___________________________________________________ Microscope Worksheet Activity 1. Becoming Familiar with the Microscope Sketch the cork sample under 10X and 40X objectives. Objective Magnification __________ Objective Magnification __________ Ocular Magnification __________ Ocular Magnification __________ Total Magnification __________ Total Magnification __________ Activity 2. Estimating Crystal Size Salt Sugar Objective Magnification __________ Objective Magnification __________ Ocular Magnification __________ Ocular Magnification __________ Total Magnification __________ Total Magnification __________ Trial 1 __________ Trial 1 __________ Trial 2 __________ Trial 2 __________ Trial 3 __________ Trial 3 __________ Average Size __________ Average Size __________ Activity 3. Preparing a Wet Mount with Newsprint Objective Magnification __________ Naked eye Ocular Magnification __________ Total Magnification __________ Activity 4. Finding and Identifying Microorganisms Sketch and name three microorganisms located under the microscope. Objective Magnification __________ Objective Magnification __________ Objective Magnification __________ Ocular Magnification __________ Ocular Magnification __________ Ocular Magnification __________ Total Magnification __________ Total Magnification __________ Total Magnification __________ Organism name __________ Organism name __________ Organism name __________ © 2018, Flinn Scientific, Inc. All Rights Reserved. Reproduction permission is granted from Flinn Scientific, Inc. Batavia, Illinois, U.S.A. -
Predator-Prey Interactions Between the Ciliate Blepharisma Americanum
Vol. 83: 211–224, 2019 AQUATIC MICROBIAL ECOLOGY Published online September 19 https://doi.org/10.3354/ame01913 Aquat Microb Ecol OPENPEN ACCESSCCESS Predator−prey interactions between the ciliate Blepharisma americanum and toxic (Microcystis spp.) and non-toxic (Chlorella vulgaris, Microcystis sp.) photosynthetic microbes Ian J. Chapman1,2, Daniel J. Franklin1, Andrew D. Turner3, Eddie J. A. McCarthy1, Genoveva F. Esteban1,* 1Bournemouth University, Department of Life and Environmental Sciences, Faculty of Science and Technology, Dorset, BH12 5BB, UK 2NSW Shellfish Program, NSW Food Authority, Taree, NSW 2430, Australia 3Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Weymouth, Dorset, DT4 8UB, UK ABSTRACT: Despite free-living protozoa being a major factor in modifying aquatic autotrophic biomass, ciliate−cyanobacteria interactions and their functional ecological roles have been poorly described, especially with toxic cyanobacteria. Trophic relationships have been neglected and grazing experiments give contradictory evidence when toxic taxa such as Microcystis are in - volved. Here, 2 toxic Microcystis strains (containing microcystins), 1 non-toxic Microcystis strain and a non-toxic green alga, Chlorella vulgaris, were used to investigate predator−prey interac- tions with a phagotrophic ciliate, Blepharisma americanum. Flow cytometric analysis for micro- algal measurements and a rapid ultra high performance liquid chromatography-tandem mass spectrometry protocol to quantify microcystins showed that non-toxic photosynthetic microbes were significantly grazed by B. americanum, which sustained ciliate populations. In contrast, despite constant ingestion of toxic Microcystis, rapid egestion of cells occurred. The lack of diges- tion resulted in no significant control of toxic cyanobacteria densities, a complete reduction in cil- iate numbers, and no observable encystment or cannibalistic behaviour (gigantism).