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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. -
Effects of Temperature, Light Intensity and Quality, Carbon Dioxide, and Culture Medium Nutrients on Growth and Lipid Production of Ettlia Oleoabundans
Effects of Temperature, Light Intensity and Quality, Carbon Dioxide, and Culture Medium Nutrients on Growth and Lipid Production of Ettlia oleoabundans by Ying Yang A Dissertation Submitted to the Faculty of WORCESTER POLYTECHNIC INSTITUTE in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology and Biotechnology by December 2013 Approved by: Dr. Pamela Weathers, Advisor Dr. Robert Thompson, Committee Member Dr. Luis Vidali, Committee Member Dr. Reeta Rao, Committee Member “A journey of a thousand miles begins with a single step.” — Lao Tzu (604 BC – 531 BC) ii Abstract Ettlia oleoabundans, a freshwater green microalga, was grown under different environmental conditions to study its growth, lipid yield and quality for a better understanding of the fundamental physiology of this oleaginous species. E. oleoabundans showed steady increase in biomass under low temperature and low light intensity, and at high temperature lipid cell content significantly increased independent of nitrate depletion. Studies on light quality showed that red light treatment did not change the biomass concentration, but stimulated lipid yield especially oleic acid, the most desirable biodiesel precursor. Moreover, no photoreversibility in lipid production was observed when applying alternating short-term red and far-red lights, which left the phytochrome effect still an open question. In addition, carbon dioxide enrichment via an air sparging system significantly boosted exponential growth and increased carbon conversion efficiency. Finally, a practical study demonstrated the feasibility of growing E. oleoabundans for high lipid production using a diluted agricultural anaerobic waste effluent as the medium. Together, these studies showed the potential of E. oleoabundans as a promising high yield feedstock for the production of high quality biodiesel. -
Bangor University DOCTOR of PHILOSOPHY
Bangor University DOCTOR OF PHILOSOPHY Studies on micro algal fine-structure, taxonomy and systematics : cryptophyceae and bacillariophyceae. Novarino, Gianfranco Award date: 1990 Link to publication 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 ? Take down policy 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. Download date: 02. Oct. 2021 Studies on microalgal fine-structure, taxonomy, and systematics: Cryptopbyceae and Bacillariopbyceae In Two Volumes Volume I (Text) ,, ý,ý *-ýýI Twl by Gianfranco Novarino, Dottore in Scienze Biologiche (Rom) A Thesis submitted to the University of Wales in candidature for the degree of Philosophiae Doctor University of Wales (Bangor) School of Ocean Sciences Marine Science Laboratories Menai Bridge, Isle of Anglesey, United Kingdom December 1990 Lýýic. JýýVt. BEST COPY AVAILABLE Acknowledge mehts Dr I. A. N. Lucas, who supervised this work, kindly provided his helpful guidance, sharing his knowledge and expertise with patience and concern, critically reading the manuscripts of papers on the Cryptophyceae, and supplying many starter cultures of the strains studied here. -
DIMITAR VALEV: Wastewater Treatment with Algae Doctoral Dissertation, 118 Pp
ANNALES UNIVERSITATIS TURKUENSIS UNIVERSITATIS ANNALES AI 627 AI Dimitar Valev WASTEWATER TREATMENT WITH ALGAE Dimitar Valev Painosalama Oy, Turku, Finland 2020 Finland Turku, Oy, Painosalama ISBN 978-951-29-8094-9 (PRINT) – ISBN 978-951-29-8095-6 (PDF) TURUN YLIOPISTON JULKAISUJA ANNALES UNIVERSITATIS TURKUENSIS ISSN 0082-7002 (Print) SARJA – SER. AI OSA – TOM. 627 | ASTRONOMICA – CHEMICA – PHYSICA – MATHEMATICA | TURKU 2020 ISSN 2343-3175 (Online) WASTEWATER TREATMENT WITH ALGAE Dimitar Valev TURUN YLIOPISTON JULKAISUJA – ANNALES UNIVERSITATIS TURKUENSIS SARJA – SER. AI OSA – TOM. 627 | ASTRONOMICA – CHEMICA – PHYSICA – MATHEMATICA | TURKU 2020 University of Turku Faculty of Science and Engineering Department of Biochemistry / Molecular Plant Biology Doctoral programme in Molecular Life Sciences Supervised by Dr. Esa Tyystjärvi Dr. Taina Tyystjärvi Department of Biochemistry / Department of Biochemistry / Molecular Plant Biology, Molecular Plant Biology, University of Turku, FI-20014 University of Turku, FI-20014 Turku, Finland Turku, Finland Dr. Taras Antal Department of Botany and Plant Ecology Pskov State University Pskov 180000 Russia Reviewed by Professor Amit Bhatnagar Professor Koenraad Muylaert Water Chemistry & Microbiology Laboratory of Aquatic Biology University of Eastern Finland KU Leuven Kuopio, Finland Kortrijk, Belgium Opponent Professor Ondřej Prášil Centre Algatech Institute of Microbiology, The Czech Academy of Sciences Třeboň, Czech Republic The originality of this publication has been checked in accordance with the University of Turku quality assurance system using the Turnitin OriginalityCheck service. ISBN 978-951-29-8094-9 (PRINT) ISBN 978-951-29-8095-6 (PDF) ISSN 0082-7002 (Painettu/Print) ISSN 2343-3175 (Sähköinen/Online) Painosalama Oy, Turku, Finland 2020 UNIVERSITY OF TURKU Faculty of Science and Engineering Department of Biochemistry Molecular Plant Biology DIMITAR VALEV: Wastewater treatment with algae Doctoral Dissertation, 118 pp. -
Lake Spokane Dissolved Oxygen Water Quality Attainment Plan Five Year Report
AVISTA CORPORATION LAKE SPOKANE DISSOLVED OXYGEN WATER QUALITY ATTAINMENT PLAN FIVE YEAR REPORT WASHINGTON 401 CERTIFICATION FERC LICENSE APPENDIX B, SECTION 5.6 SPOKANE RIVER HYDROELECTRIC PROJECT FERC PROJECT NO. 2545 Prepared By: March 24, 2017 [Page intentionally left blank] TABLE OF CONTENTS 1.0 INTRODUCTION ........................................................................................................ 1 2.0 BASELINE MONITORING ........................................................................................ 3 2.1 2016 Monitoring Results .............................................................................................. 3 2.2 Assessment of Lake Spokane Water Quality (2010 – 2016) ........................................ 7 2.3 Monitoring Recommendations ..................................................................................... 8 3.0 IMPLEMENTATION ACTIVITIES ........................................................................... 9 3.1 Studies .......................................................................................................................... 9 3.1.1 Carp Population Reduction Program ...................................................................... 10 3.1.2 Aquatic Weed Management .................................................................................... 10 3.2 2016 Implementation Measures .................................................................................. 11 3.2.1 Carp ........................................................................................................................ -
Compartmentalization of Mrnas in the Giant, Unicellular Green Algae
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.18.303206; this version posted September 18, 2020. 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 Compartmentalization of mRNAs in the giant, 2 unicellular green algae Acetabularia acetabulum 3 4 Authors 5 Ina J. Andresen1, Russell J. S. Orr2, Kamran Shalchian-Tabrizi3, Jon Bråte1* 6 7 Address 8 1: Section for Genetics and Evolutionary Biology, Department of Biosciences, University of 9 Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316 Oslo, Norway. 10 2: Natural History Museum, University of Oslo, Oslo, Norway 11 3: Centre for Epigenetics, Development and Evolution, Department of Biosciences, University 12 of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316 Oslo, Norway. 13 14 *Corresponding author 15 Jon Bråte, [email protected] 16 17 Keywords 18 Acetabularia acetabulum, Dasycladales, UMI, STL, compartmentalization, single-cell, mRNA. 19 20 Abstract 21 Acetabularia acetabulum is a single-celled green alga previously used as a model species for 22 studying the role of the nucleus in cell development and morphogenesis. The highly elongated 23 cell, which stretches several centimeters, harbors a single nucleus located in the basal end. 24 Although A. acetabulum historically has been an important model in cell biology, almost 25 nothing is known about its gene content, or how gene products are distributed in the cell. To 26 study the composition and distribution of mRNAs in A. -
The Ecology and Glycobiology of Prymnesium Parvum
The Ecology and Glycobiology of Prymnesium parvum Ben Adam Wagstaff This thesis is submitted in fulfilment of the requirements of the degree of Doctor of Philosophy at the University of East Anglia Department of Biological Chemistry John Innes Centre Norwich September 2017 ©This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that use of any information derived there from must be in accordance with current UK Copyright Law. In addition, any quotation or extract must include full attribution. Page | 1 Abstract Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms (HABs) globally, leading to large scale fish kills that have severe ecological and economic implications. A HAB on the Norfolk Broads, U.K, in 2015 caused the deaths of thousands of fish. Using optical microscopy and 16S rRNA gene sequencing of water samples, P. parvum was shown to dominate the microbial community during the fish-kill. Using liquid chromatography-mass spectrometry (LC-MS), the ladder-frame polyether prymnesin-B1 was detected in natural water samples for the first time. Furthermore, prymnesin-B1 was detected in the gill tissue of a deceased pike (Exos lucius) taken from the site of the bloom; clearing up literature doubt on the biologically relevant toxins and their targets. Using microscopy, natural P. parvum populations from Hickling Broad were shown to be infected by a virus during the fish-kill. A new species of lytic virus that infects P. parvum was subsequently isolated, Prymnesium parvum DNA virus (PpDNAV-BW1). -
Structural Variation and Evolution of Chloroplast Trnas in Green Algae
Structural variation and evolution of chloroplast tRNAs in green algae Fangbing Qi, Yajing Zhao, Ningbo Zhao, Kai Wang, Zhonghu Li and Yingjuan Wang State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotech- nology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China ABSTRACT As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28–32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23–27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the 9-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. -
Chloroplast Phylogenomic Analysis of Chlorophyte Green Algae Identifies a Novel Lineage Sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T
Lemieux et al. BMC Evolutionary Biology (2015) 15:264 DOI 10.1186/s12862-015-0544-5 RESEARCHARTICLE Open Access Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae) Claude Lemieux*, Antony T. Vincent, Aurélie Labarre, Christian Otis and Monique Turmel Abstract Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. -
Enrichment of Bioactive Compounds in Microalgae for Aquaculture
Enrichment of Bioactive Compounds in Microalgae for Aquaculture Tese apresentada à Universidade da Madeira com vista à obtenção do grau de Mestre em Bioquímica Aplicada Tomásia Micaela Gomez Fernandes Sob a orientação de: Professora Doutora Nereida Maria Abano Cordeiro Doutor Carlos Alberto Pestana Andrade Faculdade de Ciências Exatas e da Engenharia Universidade da Madeira Funchal – Portugal Centro de Maricultura da Calheta Calheta – Portugal Dezembro 2015 Acknowledgments Throughout the execution of this work many were the people who support me with their enthusiasm and collaboration. To my supervisor Prof. Dr. Nereida Cordeiro for accept this challenge and for guiding me during the development of the project. And to whom I also show my appreciation for the motivation showed. To my co-supervisor Dr. Carlos Andrade for its availability in clarifying any questions and for supplying the materials in the course of this work project. To the laboratory technician José Faria for his help and readiness in autoclaving the lab material and culture medium, and for providing the reagents and lab material each time I needed. I am also grateful to Bernardo Sumares for his help, availability and for providing the materials at the mariculture center. To Prof. Dr. Helena Tomás for having made available the microscope for the photomicrographs. I would like to acknowledge Igor Fernandes for his endless support, love, understanding, encouraging and precious collaboration in the work developed. To my friends and coleagues Cátia Vieira, Emanuel Gouveia, Dina Maciel, Marisa Faria, Marta Rodrigues, Roberto Aguiar and Sónia Nóbrega for their friendship, motivation and concern. A special thanks to Emanuel and Roberto for their help in the work project. -
Concordance of Molecular and Ultrastructural Data in the Study of Zoosporic Chlorococcalean Green Algae'
/ Phycol. 28, 375-380 (1992) CONCORDANCE OF MOLECULAR AND ULTRASTRUCTURAL DATA IN THE STUDY OF ZOOSPORIC CHLOROCOCCALEAN GREEN ALGAE' Louise A. Lewis,^ Lee W. Wilcox, Paul A. Fuerst,* and Gary L. Floyd^ Departments of Plant Biology and *Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 ABSTRACT Ultrastructural studies have led to reconsidera- Alternative evolutionary hypotheses generated from fea- tion of several morphologically based groups and tures of vegetative cell morphology and motile cell ultra- resulted in the separation of the green algae into structure were investigated using a molecular data set. five classes (Pickett-Heaps 1975, Moestrup 1978, Complete nuclear-encoded small subunit (18S) ribosomai Stewart and Mattox 1978, Melkonian 1982, Floyd RNA (rRNA) gene sequences were determined for six spe- and O'Kelly 1984, Mattox and Stewart 1984, O'Kel- cies (three each) of the chlorococcalean green algae "Neo- ly and Floyd 1984, Sluiman 1989). Through these chloris" and Characium. Based on motile cell ultra- studies it became apparent that many of the tradi- structure, it was previously shown that both genera could tional groupings based on vegetative cell morphol- be separated into three distinct groups possibly represent- ogy contained genera that cut across the newly pro- ing three separate orders and two classes of green algae. posed class boundaries and that certain characters 18S rRNA gene sequences were also obtained for three probably reflected parallel changes. additional taxa, Dunaliella parva Lerche, Pediastrum Two recent examples of the apparent discordance duplex Meyen, and Friedmannia israelensis Chanta- between vegetative morphological and ultrastruc- nachat and Bold. These organisms were selected because tural classifications involve chlorococcalean genera each, in turn, is a representative of one of the three ul- that are vegetatively non-motile but produce motile trastructural groups into which the Neochloris and zoospores. -
Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) Inferred from 18S Rdna Sequences with Emphasis on the Relationships in Th
Pl. Syst. Evol. 265: 179–191 (2007) Plant Systematics DOI 10.1007/s00606-007-0523-4 and Evolution Printed in The Netherlands Phylogeny of Oedogoniales (Chlorophyceae, Chlorophyta) inferred from 18S rDNA sequences with emphasis on the relationships in the genus Oedogonium based on ITS-2 sequences H. Mei1,2, W. Luo3,4, G. X. Liu1, and Z. Y. Hu1 1State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan, China 2Graduated School, the Chinese Academy of Sciences, Beijing, China 3Leibniz Institute of Freshwater Ecology and Inland Fisheries, Department of Limnology of Stratified Lakes, Stechlin - Neuglobsow, Germany 4SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China Received March 6, 2006; accepted January 22, 2007 Published online: May 14, 2007 Ó Springer-Verlag 2007 Abstract. The phylogeny of Oedogoniales was Introduction investigated by using nuclear 18S rDNA sequences. Results showed that the genus Oedocladium,asa The Oedogoniales, comprised of three genera separated clade, was clustered within the clade of (Oedogonium, Oedocladium and Bulbochaete), Oedogonium; whereas the genus Bulbochaete was in can be found in freshwater all over the world a comparatively divergent position to the other two (Hirn 1900, Tiffany 1937, Gemeinhardt 1939, genera. The relationship among the species of Gauthie´ r-Lie` vre 1963, Islam and Sarma 1963, Oedogonium was discussed, focusing on ITS-2 Jao 1979, Mrozin´ ska 1985). Their fascinating phylogeny analyzed combining with some morpho- and distinctive features that are well known to logical characteristics. Our results showed that all phycologists set them apart into a very unusual the dioecious nannandrous taxa involved in this order of green algae.