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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. -
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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Producing Gambierdiscus Polynesiensis and G.Excentricus (Dinophyceae) Kohli, G
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Queen's University Research Portal Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-producing Gambierdiscus polynesiensis and G.excentricus (Dinophyceae) Kohli, G. S., Campbell, K., John, U., Smith, K. F., Fraga, S., Rhodes, L. L., & Murray, S. A. (2017). Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-producing Gambierdiscus polynesiensis and G.excentricus (Dinophyceae). DOI: 10.1111/jeu.12405 Published in: The Journal of Eukaryotic Microbiology Document Version: Peer reviewed version Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights Copyright Wiley 2017. This work is made available online in accordance with the publisher’s policies. Please refer to any applicable terms of use of the publisher. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. If you discover content in the Research Portal that you believe breaches copyright or violates any law, please contact [email protected]. -
Universidade Federal Do Estado Do Rio De Janeiro
UNIVERSIDADE FEDERAL DO ESTADO DO RIO DE JANEIRO - UNIRIO CENTRO DE CIÊNCIAS BIOLÓGICAS E DA SAÚDE - CCBS INSTITUTO DE BIOCIÊNCIAS - IBio PROGRAMA DE PÓS-GRADUAÇÃO EM CIÊNCIAS BIOLÓGICAS - PPGBIO (BIODIVERSIDADE NEOTROPICAL) Erick Alves Pereira Lopes Filho Filogenia e filogeografia de espécies de Dictyota Lamouroux (Dictyotales: Phaeophyceae) Rio de Janeiro 2018 Erick Alves Pereira Lopes Filho Filogenia e filogeografia de espécies de Dictyota Lamouroux (Dictyotales: Phaeophyceae) Dissertação apresentada ao Programa de Pós-Graduação em Ciências Biológicas (Biodiversidade Neotropical) da Universidade Federal do Estado do Rio de Janeiro como requisito parcial para obtenção do título de Mestre. Orientador: Prof. Dr. Joel Campos de Paula Co-orientador: Prof. Dr. Fabiano Salgueiro Rio de Janeiro 2018 UNIVERSIDADE FEDERAL DO ESTADO DO RIO DE JANEIRO - UNIRIO CENTRO DE CIÊNCIAS BIOLÓGICAS E DA SAÚDE - CCBS INSTITUTO DE BIOCIÊNCIAS - IBio Erick Alves Pereira Lopes Filho Filogenia e filogeografia de espécies de Dictyota Lamouroux (Dictyotales: Phaeophyceae) Dissertação apresentada ao curso de Mestrado em Ciências Biológicas do Programa de Pós- Graduação em Ciências Biológicas (Biodiversidade Neotropical) da Universidade Federal do Estado do Rio de Janeiro no dia 11 de janeiro de 2018, como requisito parcial para a obtenção do título de Mestre em Ciências Biológicas. A mesma foi avaliada pela banca examinadora composta por Dr.ª Maria Beatriz Barbosa de Barros Barreto, Dr.ª Valéria Cassano e Dr. Joel Campos de Paula, sendo suplentes Dr. Fabiano Salgueiro, Dr. Leandro Pederneiras e Dr.ª Valéria Laneuville Teixeira, e aprovada com o conceito _________________ Dr.ª Maria Beatriz Barbosa de Barros Barreto Universidade Federal do Rio de Janeiro ______ Dr.ª Valéria Cassano Universidade de São Paulo Dr. -
Morphology, Molecular Phylogeny and Toxinology of Coolia And
Botanica Marina 2019; 62(2): 125–140 Maria Cristina de Queiroz Mendes*, José Marcos de Castro Nunes, Santiago Fraga, Francisco Rodríguez, José Mariano Franco, Pilar Riobó, Suema Branco and Mariângela Menezes Morphology, molecular phylogeny and toxinology of Coolia and Prorocentrum strains isolated from the tropical South Western Atlantic Ocean https://doi.org/10.1515/bot-2018-0053 P. emarginatum by mass spectrometry analyses. However, Received 19 May, 2018; accepted 14 February, 2019; online first hemolytic assays in P. emarginatum and both Coolia strains 13 March, 2019 in this study showed positive results. Abstract: The morphology, molecular phylogeny and toxi- Keywords: Coolia malayensis; Coolia tropicalis; hemolytic nology of two Coolia and one Prorocentrum dinoflagellate assay; LC-HRMS; Prorocentrum emarginatum. strains from Brazil were characterized. They matched with Coolia malayensis and Coolia tropicalis morphotypes, while the Prorocentrum strain fitted well with the morphology of Prorocentrum emarginatum. Complementary identification Introduction by molecular analyses was carried out based on LSU and ITS-5.8S rDNA. Phylogenetic analyses of Coolia strains (D1/ Epibenthic dinoflagellate communities harbor potentially D2 region, LSU rDNA), showed that C. malayensis (strain harmful species that attracted great interest in the last UFBA044) segregated together with sequences of this spe- decades due to their apparent expansion from tropical/ cies from other parts of the world, but diverged earlier in subtropical areas to temperate -
Mixotrophic Protists Among Marine Ciliates and Dinoflagellates: Distribution, Physiology and Ecology
FACULTY OF SCIENCE UNIVERSITY OF COPENHAGEN PhD thesis Woraporn Tarangkoon Mixotrophic Protists among Marine Ciliates and Dinoflagellates: Distribution, Physiology and Ecology Academic advisor: Associate Professor Per Juel Hansen Submitted: 29/04/10 Contents List of publications 3 Preface 4 Summary 6 Sammenfating (Danish summary) 8 สรุป (Thai summary) 10 The sections and objectives of the thesis 12 Introduction 14 1) Mixotrophy among marine planktonic protists 14 1.1) The role of light, food concentration and nutrients for 17 the growth of marine mixotrophic planktonic protists 1.2) Importance of marine mixotrophic protists in the 20 planktonic food web 2) Marine symbiont-bearing dinoflagellates 24 2.1) Occurrence of symbionts in the order Dinophysiales 24 2.2) The spatial distribution of symbiont-bearing dinoflagellates in 27 marine waters 2.3) The role of symbionts and phagotrophy in dinoflagellates with symbionts 28 3) Symbiosis and mixotrophy in the marine ciliate genus Mesodinium 30 3.1) Occurrence of symbiosis in Mesodinium spp. 30 3.2) The distribution of marine Mesodinium spp. 30 3.3) The role of symbionts and phagotrophy in marine Mesodinium rubrum 33 and Mesodinium pulex Conclusion and future perspectives 36 References 38 Paper I Paper II Paper III Appendix-Paper IV Appendix-I Lists of publications The thesis consists of the following papers, referred to in the synthesis by their roman numerals. Co-author statements are attached to the thesis (Appendix-I). Paper I Tarangkoon W, Hansen G Hansen PJ (2010) Spatial distribution of symbiont-bearing dinoflagellates in the Indian Ocean in relation to oceanographic regimes. Aquat Microb Ecol 58:197-213. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley, -
Ball Et Al. (2011)
Journal of Experimental Botany, Vol. 62, No. 6, pp. 1775–1801, 2011 doi:10.1093/jxb/erq411 Advance Access publication 10 January, 2011 DARWIN REVIEW The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis Steven Ball*, Christophe Colleoni, Ugo Cenci, Jenifer Nirmal Raj and Catherine Tirtiaux Unite´ de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Baˆ timent C9, Cite´ Scientifique, F-59655 Villeneuve d’Ascq, France * To whom correspondence should be addressed: E-mail: [email protected] Received 10 September 2010; Revised 18 November 2010; Accepted 23 November 2010 Downloaded from Abstract Solid semi-crystalline starch and hydrosoluble glycogen define two distinct physical states of the same type of storage polysaccharide. Appearance of semi-crystalline storage polysaccharides appears linked to the http://jxb.oxfordjournals.org/ requirement of unicellular diazotrophic cyanobacteria to fuel nitrogenase and protect it from oxygen through respiration of vast amounts of stored carbon. Starch metabolism itself resulted from the merging of the bacterial and eukaryote pathways of storage polysaccharide metabolism after endosymbiosis of the plastid. This generated the three Archaeplastida lineages: the green algae and land plants (Chloroplastida), the red algae (Rhodophyceae), and the glaucophytes (Glaucophyta). Reconstruction of starch metabolism in the common ancestor of Archaeplastida suggests that polysaccharide synthesis was ancestrally cytosolic. In addition, the synthesis of cytosolic starch from the ADP-glucose exported from the cyanobacterial symbiont possibly defined the original by guest on March 30, 2012 metabolic flux by which the cyanobiont provided photosynthate to its host. Additional evidence supporting this scenario include the monophyletic origin of the major carbon translocators of the inner membrane of eukaryote plastids which are sisters to nucleotide-sugar transporters of the eukaryote endomembrane system. -
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. -
The Nitrogen-Fixing Symbiotic Cyanobacterium, Nostoc Punctiforme Can Regulate Plant Programmed Cell Death
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.13.249318; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The nitrogen-fixing symbiotic cyanobacterium, Nostoc punctiforme can regulate plant programmed cell death Samuel P. Belton1,4, Paul F. McCabe1,2,3, Carl K. Y. Ng1,2,3* 1UCD School of Biology and Environmental Science, 2UCD Centre for Plant Science, 3UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin, DN04 E25, Republic of Ireland 4Present address: DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin, D09 E7F2, Republic of Ireland *email: [email protected] Acknowledgements This work was financially supported by a Government of Ireland Postgraduate Scholarship from the Irish Research Council (GOIPG/2015/2695) to SPB. Author contributions S.P.B., P.F.M, and C.K.Y.N conceived of the study and designed the experiments. S.B. performed all the experiments and analysed the data. S.B. prepared the draft of the manuscript with the help of P.F.M and C.K.Y.N. All authors read, edited, and approved the manuscript. Competing interests The authors declare no competing interests. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.13.249318; this version posted August 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Cyanobacteria such as Nostoc spp. -
Dictyota Adnata Zanardini (Phaeophyceae) - a New Record from the Sundarbans Mangrove Forests, Bangladesh
Bangladesh J. Bot. 49(2): 407-412, 2020 (June) - Short communication DICTYOTA ADNATA ZANARDINI (PHAEOPHYCEAE) - A NEW RECORD FROM THE SUNDARBANS MANGROVE FORESTS, BANGLADESH 1 2 MD ARIFUL ISLAM, MD RASHEDUL ISLAM , ABDUL AZIZ AND LAWRENCE M LIAO* Aquatic Botany Laboratory, Department of Bioresource Science, Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Japan 739-8528 Keywords: Brown algae, Epiphyte, Phycology, Taxonomy, A new record Abstract Samples were collected from Arpangasia and Kholpetua rivers within the Sundarbans in Bangladesh during February to March and December 2018. Among several forms was found a tightly prostrate brown alga occurring on moist parts of mangrove plants and clayey soil. Flattened brownish thalli tightly attached to pneumatophores and lower parts of mangrove trunks, spreading and branching dichotomously, sometimes overlapping and attached by means of unbranched marginal and sub-marginal rhizoids were collected. Distinct marginal sori are well developed in fertile specimens. On the basis of these characters, the sample has been identified as Dictyota adnata Zanardini which is herein reported as a new record for Bangladesh. The Sundarbans is the world’s largest mangrove ecosystem that is shared by India and Bangladesh fronting the vast Bay of Bengal to the south representing a unique ecosystem showcasing an astounding floral and faunal assemblage that is constantly exposed to various anthropogenic and natural threats (Aziz and Paul 2015). The rich biodiversity and largest contiguous forests of the Sundarbans were recognized when large portions of it were designated as a UNESCO World Heritage Site as well as a Ramsar site. The algal flora within the Sundarbans was first studied by Islam (1973) who documented 35 species, most of them belonging to the “Bostrychietum” group. -
Eighth International Conference on Modern and Fossil Dinoflagellates
0 DINO8 Eighth International Conference on Modern and Fossil Dinoflagellates May 4 to May 10, 2008 Université du Québec à Montréal Complexe des Sciences Pierre Dansereau Building SH, 200 Sherbrooke Street West, Montreal, Quebec, Canada Abstracts 1 TABLE OF CONTENTS ABSTRACTS……………………………………………………………………………………...2 LIST OF PARTICIPANTS………………………………………………………………………66 Organizing commitee Organizers : Anne de Vernal GEOTOP-UQAM, Canada ([email protected]) André Rochon ISMER-UQAR, Canada ([email protected]) Scientific committee: Susan Carty, Heidelberg College, Ohio, USA ([email protected]) Lucy Edwards, US Geological Survey ([email protected]) Marianne Ellegaard, University of Copenhagen, Denmark ([email protected]) Martin J. Head, Brock University, Canada ([email protected]) Alexandra Kraberg, Alfred Wegener Institute for Polar and Marine Research, Germany ([email protected] ) Jane Lewis, University of Westminster, UK ([email protected] ) Fabienne Marret, University of Liverpool, UK ([email protected] ) Kazumi Matsuoka, University of Nagasaki, Japan ([email protected] ) Jens Matthiessen, Alfred Wegener Institute for Polar and Marine Research, Germany ([email protected] ) Edwige Masure, Université Pierre et Marie Curie, France ([email protected] ) Marina Montresor, Stazione zoologica "Anton Dohrn" di Napoli, Italy ([email protected] ) Vera Pospelova, University of Victoria, Canada ([email protected] ) Suzanne Roy, ISMER-UQAR, Canada ([email protected]) Karin Zonneveld, University of Bremen, Germany ([email protected]) 2 ABSTRACTS Toxic blooms of Alexandrium fundyense in the Monitoring of the regional abundance of cysts may Gulf of Maine: the role of cysts in population thus hold the key to interannual forecasts of A. dynamics and long-term patterns of shellfish fundyense bloom severity in this region.