Biologia Celular – Cell Biology
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Handout Lec. 25
Introduction to Biosystematics - Zool 575 Introduction to Biosystematics Confidence - Assessment of the Strength of Lecture 25 - Confidence - Assessment 2 the Phylogenetic Signal - part 2 1. Consistency Index 2. g1 statistic, PTP - test “Quantifying the uncertainty of a phylogenetic 3. Consensus trees estimate is at least as important a goal as obtaining the phylogenetic estimate itself.” 4. Decay index (Bremer Support) - Huelsenbeck & Rannala (2004) 5. Bootstrapping / Jackknifing 6. Statistical hypothesis testing (frequentist) 7. Posterior probability (see lecture on Bayesian) Derek S. Sikes University of Calgary Zool 575 Multiple optimal trees Multiple optimal trees • Many methods can yield multiple equally • If multiple optimal trees are found we know optimal trees that all of them are wrong except, possibly, (hopefully) one • We can further select among these trees with additional criteria, but • Some have argued against consensus tree methods for this reason • Typically, relationships common to all the optimal trees are summarized with • Debate over quest for true tree (point consensus trees estimate) versus quantification of uncertainty Consensus methods Strict consensus methods • A consensus tree is a summary of the agreement • Strict consensus methods require agreement among a set of fundamental trees across all the fundamental trees • There are many consensus methods that differ in: • They show only those relationships that are 1. the kind of agreement unambiguously supported by the data 2. the level of agreement • The commonest -
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. -
Organelle Movement in Actinophrys Soland Its Inhibition by Cytochalasin B
Acta Protozool. (2003) 42: 7 - 10 Organelle Movement in Actinophrys sol and Its Inhibition by Cytochalasin B Toshinobu SUZAKI1, Mikihiko ARIKAWA1, Akira SAITO1, Gen OMURA1, S. M. Mostafa Kamal KHAN1, Miako SAKAGUCHI2,3 and Klaus HAUSMANN3 1Department of Biology, Faculty of Science; 2Research Institute for Higher Education, Kobe University, Kobe, Japan; 3Institute of Biology/Zoology, Free University of Berlin, Berlin, Germany Summary. Movement of extrusomes in the heliozoon Actinophrys sol was characterized at surfaces of the cell body and giant food vacuoles where microtubules are absent. Extrusomes moved in a saltatory manner at an average velocity of 0.5 µms-1. The highest velocity observed was 2.1 µms-1. Cytochalasin B (50 µg/ml) strongly inhibited extrusome movement at the surfaces of newly-formed food vacuoles, suggesting that the actomyosin system is involved in the organelle transport in Actinophrys. Key words: actinophryid, actomyosin, extrusome, heliozoa, organelle transport. INTRODUCTION Edds (1975a) showed that organelle movement of the heliozoon Echinosphaerium still occurred in artificial Transport of intracellular organelles is a ubiquitous axopodia where a glass microneedle substituted for the feature of eukaryotic cells (e.g. Rebhun 1972, Hyams microtubular axoneme, and colchicine did not inhibit the and Stebbings 1979, Schliwa 1984). In many instances, motion in either the normal or the artificial axopodia microtubules have been postulated as important ele- (Tilney 1968, Edds 1975a). Organelle movement is also ments along which bidirectional particle transport takes known to take place in the cortex of the heliozoon cell place (Koonce and Schliwa 1985, Hayden and Allen body where no microtubules are present (Fitzharris et al. -
Geotaxis in the Ciliated Protozoon Loxodes
J. exp. Biol. 110, 17-33 (1984) 17 d in Great Britain © The Company of Biologists Limited 1984 GEOTAXIS IN THE CILIATED PROTOZOON LOXODES BY T. FENCHEL Department of Ecology and Genetics, University ofAarhus, DK-8000 Aarhus, Denmark AND B. J. FINLAY Freshwater Biological Association, The Ferry House, Ambleside, Cumbria LA22 OLP, U.K. Accepted 14 November 1983 SUMMARY Geotaxis is demonstrated in the ciliated protozoon Loxodes. This behaviour is mediated by a mechanoreceptor which is probably the Muller body, an organelle characteristic of loxodid ciliates. The geotactic response is sensitive to dissolved oxygen tension: in anoxia or at very low O2 tensions the ciliates tend to swim up and at higher O2 tensions they tend to swim down. This behaviour, in conjunction with a kinetic response allows the ciliates to orientate themselves in vertical O2 gradients and to congregate in their optimum environment. In two appendices, models of the behaviour predicting vertical distribution patterns and considerations of the minimum size of a functional statocyst are offered. INTRODUCTION Many protozoa display a pronounced positive or negative geotaxis. The mechan- isms responsible for this have been the subject of a prolonged dispute (for references see Roberts, 1970). In the species studied so far, however, there is no evidence of mechanoreceptors. Rather, the geotactic behaviour can be explained as the result of the interactions between sinking velocity, swimming velocity, rate of random reorientation and the net result of gravitational and hydrodynamical forces. These tend passively to orientate the anterior end of the cells upwards. Through modulations of the swimming velocity and the rate of random reorientation, the cells can change their probability of moving upwards and hence their vertical distribution in the water column. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
Role of Metopus Es in the Anaerobic Degradation of Organic Matter and Biomethanation Process
Role of Metopus es in the anaerobic degradation of organic matter and biomethanation process Thesis submitted to the University of Kerala for award of the degree of Doctor of Philosophy in Microbiology By Nimi Narayanan Under the Supervision of Dr. V. B. Manilal Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), CSIR, Thiruvananthapuram, Kerala, INDIA - 695019 2011 To my Family DECLARATION I hereby declare that the work presented in this thesis is based on the original work done by me under the guidance of Dr. V. B. Manilal, Principal Scientist, Process Engineering and Environmental Technology Division, National Institute for Interdisciplinary Science and Technology, and that no part of this has been included in any other thesis submitted previously for the award of any degree. Nimi Narayanan Acknowledgement It is a great pleasure to express my sincere gratitude and sense of appreciation to my research guide, Dr. V.B. Manilal, Principal Scientist, Environmental Technology, NIIST, Trivandrum, for his constant encouragement, enthusiastic support and valuable guidance throughout the period of study. I am indebted to him for giving me the ample freedom to do the work and express my ideas during this period. I am grateful to Dr. Ajit Haridas, Scientist-in-charge, Environmental Technology, NIIST for his valuable suggestions and constructive criticism during my tenure. It is an honor for me to thank the present Director, Dr. Suresh Das and the former directors of NIIST, Trivandrum for providing the necessary infrastructural facilities for the successful completion of work. I would like to thank Council of Scientific and Industrial Research, New Delhi, for the research fellowship. -
Morphology and Phylogeny of the Soil Ciliate Metopus Yantaiensis N. Sp
Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Morphology and Phylogeny of the Soil Ciliate Metopus yantaiensis n. sp. (Ciliophora, Metopida), with Identification of the Intracellular Bacteria Atef Omara,b, Qianqian Zhanga, Songbao Zoua,c & Jun Gonga,c a Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China b Department of Zoology, Al-Azhar University, Assiut 71524, Egypt c University of Chinese Academy of Sciences, Beijing 100049, China Keywords ABSTRACT Anaerobic ciliates; Armophorea; digestion- resistant bacteria; Metopus contortus; The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., Metopus hasei. discovered in coastal soil of northern China, were investigated. It is distin- guished from its congeners by a combination of the following features: nuclear Correspondence apparatus situated in the preoral dome; 18–21 somatic ciliary rows, of which J. Gong, Yantai Institute of Coastal Zone three extend onto the preoral dome (dome kineties); three to five distinctly Research, Chinese Academy of Sciences, elongated caudal cilia, and 21–29 adoral polykinetids. The 18S rRNA genes of Yantai 264003, China this new species and two congeners, Metopus contortus and Metopus hasei, Telephone number: +86-535-2109123; were sequenced and phylogenetically analyzed. The new species is more clo- FAX number: +86-535-2109000; sely related to M. hasei and the clevelandellids than to other congeners; both e-mail: [email protected] the genus Metopus and the order Metopida are not monophyletic. In addition, the digestion-resistant bacteria in the cytoplasm of M. yantaiensis were identi- Received: 13 January 2017; revised 2 March fied, using a 16S rRNA gene clone library, sequencing, and fluorescence 2017; accepted March 8, 2017. -
Massisteria Marina Larsen & Patterson 1990
l MARINE ECOLOGY PROGRESS SERIES Vol. 62: 11-19, 1990 1 Published April 5 l Mar. Ecol. Prog. Ser. l Massisteria marina Larsen & Patterson 1990, a widespread and abundant bacterivorous protist associated with marine detritus David J. patterson', Tom ~enchel~ ' Department of Zoology. University of Bristol. Bristol BS8 IUG. United Kingdom Marine Biological Laboratory, Strandpromenaden, DK-3000 Helsinger, Denmark ABSTRACT: An account is given of Massisteria marina Larsen & Patterson 1990, a small phagotrophic protist associated with sediment particles and with suspended detrital material in littoral and oceanic marine waters. It has been found at sites around the world. The organism has an irregular star-shaped body from which radiate thin pseudopodia with extrusomes. There are 2 inactive flagella. The organism is normally sedentary but, under adverse conditions, the arms are resorbed, the flagella become active, and the organism becomes a motile non-feeding flagellate. The ecological niche occupied by this organism and its phylogenetic affinities are discussed. INTRODUCTION (Patterson & Fenchel 1985, Fenchel & Patterson 1986, 1988, V~rs1988, Larsen & Patterson 1990). Here we Much of the carbon fixed in marine ecosystems is report on a protist, Massisteria marina ', that is specifi- degraded by microbial communities and it is held that cally associated with planktonic and benthic detritus protists, especially flagellates under 10 pm in size, and appears to be widespread and common. exercise one of the principal controlling influences over bacterial growth rates and numbers (Fenchel 1982, Azam et al. 1983, Ducklow 1983, Proctor & Fuhrman MATERIALS AND METHODS 1990). Detrital aggregates, whether benthic or in the water column, may support diverse and active microbial Cultures were established by dilution series from communities that include flagellates (Wiebe & Pomeroy water samples taken in the Limfjord (Denmark), and 1972, Caron et al. -
Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the Mcmurdo Dry Valleys, Antarctica
Reference: Biol. Bull. 227: 175–190. (October 2014) © 2014 Marine Biological Laboratory Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica YUAN XU1,*†, TRISTA VICK-MAJORS2, RACHAEL MORGAN-KISS3, JOHN C. PRISCU2, AND LINDA AMARAL-ZETTLER4,5,* 1Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; 2Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, Bozeman, Montana 59717; 3Department of Microbiology, Miami University, Oxford, Ohio 45056; 4The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543; and 5Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island 02912 Abstract. We report an in-depth survey of next-genera- trends in dissolved oxygen concentration and salinity may tion DNA sequencing of ciliate diversity and community play a critical role in structuring ciliate communities. A structure in two permanently ice-covered McMurdo Dry PCR-based strategy capitalizing on divergent eukaryotic V9 Valley lakes during the austral summer and autumn (No- hypervariable region ribosomal RNA gene targets unveiled vember 2007 and March 2008). We tested hypotheses on the two new genera in these lakes. A novel taxon belonging to relationship between species richness and environmental an unknown class most closely related to Cryptocaryon conditions -
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 -
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. -
Protistology an International Journal Vol
Protistology An International Journal Vol. 10, Number 2, 2016 ___________________________________________________________________________________ CONTENTS INTERNATIONAL SCIENTIFIC FORUM «PROTIST–2016» Yuri Mazei (Vice-Chairman) Welcome Address 2 Organizing Committee 3 Organizers and Sponsors 4 Abstracts 5 Author Index 94 Forum “PROTIST-2016” June 6–10, 2016 Moscow, Russia Website: http://onlinereg.ru/protist-2016 WELCOME ADDRESS Dear colleagues! Republic) entitled “Diplonemids – new kids on the block”. The third lecture will be given by Alexey The Forum “PROTIST–2016” aims at gathering Smirnov (Saint Petersburg State University, Russia): the researchers in all protistological fields, from “Phylogeny, diversity, and evolution of Amoebozoa: molecular biology to ecology, to stimulate cross- new findings and new problems”. Then Sandra disciplinary interactions and establish long-term Baldauf (Uppsala University, Sweden) will make a international scientific cooperation. The conference plenary presentation “The search for the eukaryote will cover a wide range of fundamental and applied root, now you see it now you don’t”, and the fifth topics in Protistology, with the major focus on plenary lecture “Protist-based methods for assessing evolution and phylogeny, taxonomy, systematics and marine water quality” will be made by Alan Warren DNA barcoding, genomics and molecular biology, (Natural History Museum, United Kingdom). cell biology, organismal biology, parasitology, diversity and biogeography, ecology of soil and There will be two symposia sponsored by ISoP: aquatic protists, bioindicators and palaeoecology. “Integrative co-evolution between mitochondria and their hosts” organized by Sergio A. Muñoz- The Forum is organized jointly by the International Gómez, Claudio H. Slamovits, and Andrew J. Society of Protistologists (ISoP), International Roger, and “Protists of Marine Sediments” orga- Society for Evolutionary Protistology (ISEP), nized by Jun Gong and Virginia Edgcomb.