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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. -
COMPARISON of HEMOLYTIC ACTIVITY of Amphidinium Carterae and Amphidinium Klebsii
ENVIRONMENTAL REGULATION OF TOXIN PRODUCTION: COMPARISON OF HEMOLYTIC ACTIVITY OF Amphidinium carterae AND Amphidinium klebsii Leigh A. Zimmermann A Thesis Submitted to University of North Carolina Wilmington in Partial Fulfillment Of the Requirements for the Degree of Master of Science Center for Marine Science University of North Carolina Wilmington 2006 Approved by Advisory Committee ______________________________ ______________________________ ______________________________ Chair Accepted by _____________________________ Dean, Graduate School This thesis was prepared according to the formatting guidelines of the Journal of Phycology. TABLE OF CONTENTS ABSTRACT................................................................................................................................... iv ACKNOWLEDGEMENTS.............................................................................................................v LIST OF TABLES......................................................................................................................... vi LIST OF FIGURES ..................................................................................................................... viii INTRODUCTION ...........................................................................................................................1 METHODS AND MATERIALS.....................................................................................................6 Algal Culture........................................................................................................................6 -
Phylogenetic Relationships of the Genus Frenkelia
International Journal for Parasitology 29 (1999) 957±972 Phylogenetic relationships of the genus Frenkelia: a review of its history and new knowledge gained from comparison of large subunit ribosomal ribonucleic acid gene sequencesp N.B. Mugridge a, D.A. Morrison a, A.M. Johnson a, K. Luton a, 1, J.P. Dubey b, J. Voty pka c, A.M. Tenter d, * aMolecular Parasitology Unit, University of Technology, Sydney NSW, Australia bUS Department of Agriculture, ARS, LPSI, PBEL, Beltsville MD, USA cDepartment of Parasitology, Charles University, Prague, Czech Republic dInstitut fuÈr Parasitologie, TieraÈrztliche Hochschule Hannover, BuÈnteweg 17, D-30559 Hannover, Germany Received 3 April 1999; accepted 3 May 1999 Abstract The dierent genera currently classi®ed into the family Sarcocystidae include parasites which are of signi®cant medical, veterinary and economic importance. The genus Sarcocystis is the largest within the family Sarcocystidae and consists of species which infect a broad range of animals including mammals, birds and reptiles. Frenkelia, another genus within this family, consists of parasites that use rodents as intermediate hosts and birds of prey as de®nitive hosts. Both genera follow an almost identical pattern of life cycle, and their life cycle stages are morphologically very similar. How- ever, the relationship between the two genera remains unresolved because previous analyses of phenotypic characters and of small subunit ribosomal ribonucleic acid gene sequences have questioned the validity of the genus Frenkelia or the monophyly of the genus Sarcocystis if Frenkelia was recognised as a valid genus. We therefore subjected the large subunit ribosomal ribonucleic acid gene sequences of representative taxa in these genera to phylogenetic analyses to ascertain a de®nitive relationship between the two genera. -
Unfolding the Secrets of Coral–Algal Symbiosis
The ISME Journal (2015) 9, 844–856 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Unfolding the secrets of coral–algal symbiosis Nedeljka Rosic1, Edmund Yew Siang Ling2, Chon-Kit Kenneth Chan3, Hong Ching Lee4, Paulina Kaniewska1,5,DavidEdwards3,6,7,SophieDove1,8 and Ove Hoegh-Guldberg1,8,9 1School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia; 2University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia; 3School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia; 4The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; 5Australian Institute of Marine Science, Townsville, Queensland, Australia; 6School of Plant Biology, University of Western Australia, Perth, Western Australia, Australia; 7Australian Centre for Plant Functional Genomics, The University of Queensland, St Lucia, Queensland, Australia; 8ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia and 9Global Change Institute and ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reef- building corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and o2% of sequences having bacterial or other foreign origin. -
Growth and Grazing Rates of the Herbivorous Dinoflagellate Gymnodinium Sp
MARINE ECOLOGY PROGRESS SERIES Published December 16 Mar. Ecol. Prog. Ser. Growth and grazing rates of the herbivorous dinoflagellate Gymnodinium sp. from the open subarctic Pacific Ocean Suzanne L. Strom' School of Oceanography WB-10, University of Washington. Seattle. Washington 98195, USA ABSTRACT: Growth, grazing and cell volume of the small heterotroph~cdinoflagellate Gyrnnodin~um sp. Isolated from the open subarctic Pacific Ocean were measured as a funct~onof food concentration using 2 phytoplankton food species. Growth and lngestlon rates increased asymptotically with Increas- ing phytoplankon food levels, as did grazer cell volume; rates at representative oceanic food levels were high but below maxima. Clearance rates decreased with lncreaslng food levels when Isochrysis galbana was the food source; they increased ~vithlncreaslng food levels when Synechococcus sp. was the food source. There was apparently a grazlng threshold for Ingestion of Synechococcus: below an initial Synechococcus concentration of 20 pgC 1.' ingestion rates on this alga were very low, while above this initial concentratlon Synechococcus was grazed preferent~ally Gross growth efficiency varied between 0.03 and 0.53 (mean 0.21) and was highest at low food concentrations. Results support the hypothesis that heterotrophic d~noflagellatesmay contribute to controlling population increases of small, rap~dly-grow~ngphytoplankton specles even at low oceanic phytoplankton concentrations. INTRODUCTION as Gymnodinium and Gyrodinium is difficult or impos- sible using older preservation and microscopy tech- Heterotrophic dinoflagellates can be a significant niques; experimental emphasis has been on more component of the microzooplankton in marine waters. easily recognizable and collectable microzooplankton In the oceanic realm, Lessard (1984) and Shapiro et al. -
De Novo Transcriptome Assembly of Perkinsus Olseni Trophozoite Stimulated in Vitro with Manila Clam (Ruditapes Philippinarum) Plasma
Journal of Invertebrate Pathology 135 (2016) 22–33 Contents lists available at ScienceDirect Journal of Invertebrate Pathology journal homepage: www.elsevier.com/locate/jip De novo transcriptome assembly of Perkinsus olseni trophozoite stimulated in vitro with Manila clam (Ruditapes philippinarum) plasma Abul Farah Md. Hasanuzzaman a,b, Diego Robledo c, Antonio Gómez-Tato d, Jose A. Alvarez-Dios e, ⇑ Peter W. Harrison f, Asunción Cao g, Sergio Fernández-Boo g, Antonio Villalba g, Belén G. Pardo a, , Paulino Martínez a a Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain b Fisheries and Marine Resource Technology Discipline, Khulna University, Khulna 9208, Bangladesh c Departamento de Xenética, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain d Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain e Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain f Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom g Centro de Investigacións Mariñas (CIMA), Consellería do Medio Rural e do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain article info abstract Article history: The protistan parasite Perkinsus olseni is a deadly causative agent of perkinsosis, a molluscan disease Received 16 September 2015 affecting Manila clam (Ruditapes philippinarum), having a significant impact on world mollusc production. Revised 18 January 2016 Deciphering the underlying molecular mechanisms in R. philippinarum-P. olseni interaction is crucial for Accepted 24 January 2016 controlling this parasitosis. The present study investigated the transcriptional expression in the parasite Available online 25 January 2016 trophozoite using RNA-seq. -
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. -
Perkinsus Marinus Susceptibility and Defense-Related Activities in Eastern Oysters Crassostrea Virginica: Temperature Effects
DISEASES OF AQUATIC ORGANISMS Vol. 16: 223-234,1993 Published September 9 Dis. aquat. Org. Perkinsus marinus susceptibility and defense-related activities in eastern oysters Crassostrea virginica: temperature effects Fu-Lin E. Chu, Jerome F. La Peyre Virginia Institute of Marine Science, School of Marine Science, College of William and Mary, Gloucester Point, Virginia 23062, USA ABSTRACT. The relationship of potential defense-related cellular and humoral activities and the sus- ceptibility of eastern oysters Crassostrea virginica to the parasite Perkinsus marinus were examined at 10, 15, 20 and 25 "C. Oysters were acclimated at experimental temperatures for 20 d and then chal- lenged with R marinus. Total hemocyte counts (TC) and percentage of granulocytes (PG) 20 d after temperature acclimation were higher in oysters at high than at low acclimation temperature. Higher protein (P)and lysozyme (L) concentrations were found in oysters at 10 and 15 "C. No significant differ- ences in hemagglutination (H) titers due to temperature acclimation were observed. Infection preva- lence 46 d after challenge by R marinus was 100, 91, 46 and 23 % respectively, for oysters at 25, 20, 15 and 10 "C. Disease intensity increased with temperature. Oysters at higher temperatures had greater PG and TC and hemocyte phagocytic activity. No difference was found in TC and PG between control and challenged oysters within each temperature treatment. Bleeding may to some extent reduce TC and PG in oysters. P did not vary much among temperatures. No reduction of P in oysters was found due to P. marinuschallenge and infection. L tended to be higher in oysters at lower than at higher treat- ment temperatures. -
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. -
Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
Development of a Quantitative PCR Assay for the Detection And
bioRxiv preprint doi: https://doi.org/10.1101/544247; this version posted February 8, 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. Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae). Key words:Ciguatera fish poisoning, Gambierdiscus lapillus, Quantitative PCR assay, Great Barrier Reef Kretzschmar, A.L.1,2, Verma, A.1, Kohli, G.S.1,3, Murray, S.A.1 1Climate Change Cluster (C3), University of Technology Sydney, Ultimo, 2007 NSW, Australia 2ithree institute (i3), University of Technology Sydney, Ultimo, 2007 NSW, Australia, [email protected] 3Alfred Wegener-Institut Helmholtz-Zentrum fr Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany Abstract Ciguatera fish poisoning is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, in triplicate to determine the presence and patchiness of these species across samples from Chnoospora sp., Padina sp. -
Ecosystem State Change in the Arabian Sea Fuelled by the Recent Loss of Snow Over the Himalayan- Tibetan Plateau Region Joaquim I
www.nature.com/scientificreports OPEN Ecosystem state change in the Arabian Sea fuelled by the recent loss of snow over the Himalayan- Tibetan Plateau region Joaquim I. Goes 1 ✉ , Hongzhen Tian1,2, Helga do Rosario Gomes1, O. Roger Anderson 1, Khalid Al-Hashmi3, Sergio deRada4, Hao Luo5, Lubna Al-Kharusi6, Adnan Al-Azri7 & Douglas G. Martinson1 The recent trend of global warming has exerted a disproportionately strong infuence on the Eurasian land surface, causing a steady decline in snow cover extent over the Himalayan-Tibetan Plateau region. Here we show that this loss of snow is undermining winter convective mixing and causing stratifcation of the upper layer of the Arabian Sea at a much faster rate than predicted by global climate models. Over the past four decades, the Arabian Sea has also experienced a profound loss of inorganic nitrate. In all probability, this is due to increased denitrifcation caused by the expansion of the permanent oxygen minimum zone and consequent changes in nutrient stoichiometries. These exceptional changes appear to be creating a niche particularly favorable to the mixotroph, Noctiluca scintillans which has recently replaced diatoms as the dominant winter, bloom forming organism. Although Noctiluca blooms are non-toxic, they can cause fsh mortality by exacerbating oxygen defciency and ammonifcation of seawater. As a consequence, their continued range expansion represents a signifcant and growing threat for regional fsheries and the welfare of coastal populations dependent on the Arabian Sea for sustenance. Te Arabian Sea (AS) is a unique, low-latitude oceanic ecosystem because it is infuenced by monsoonal winds that reverse their direction seasonally1.