Genomic Signatures of Sex, Selection and Speciation in the Microbial World
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
Genetic Control of Apigenin Di-C-Glycoside Biosynthesis in Bread Wheat Grain and Their Role
Genetic control of Apigenin di-C-glycoside biosynthesis in bread wheat grain and their role as yellow pigments of Asian alkaline noodles Submitted by Grace Yasmein Wijaya This thesis is submitted to Faculty of Sciences in fulfilment of the requirements for the degree Doctor of Philosophy Faculty of Science The University of Adelaide November 2012 This book is An Answer to Prayers of a Long list of Believers I have been very blessed and loved with all of your spiritual supports, for His guidance and protections, and sincerely will not have enough to thank you all..... May you all be blessed and loved, too As I have been always, yasmein Table of Content Table of Content i List of Tables x List of Figures xiii List of Supplemental Materials xxv Summary xxx Statement of Authorship xxxiv List of Publications xxxv Acknowledgement xxxvi List of Abbreviations xxxix Chapter I: General Introduction 1 1.1 Background 1 1.2 Knowledge Gap 2 1.3 Structure of thesis 2 Chapter II: Literature review 4 2.1 Asian noodles as one of the major end-products of Australian bread wheat 4 2.2 Yellow colour of YAN 5 2.2.1 Natural Compounds that contribute to the yellow colour of YAN 5 2.2.1.1 Types of natural compounds that contributes to the yellow colour of YAN and their roles in plants and human health 5 2.2.1.2 Contribution of xanthophylls and ACGs to the yellow colour of alkaline noodles 8 2.2.2 Factors influencing the measurement of the yellowness of noodles and the content of xanthophyll and ACG in wheat grain 10 i 2.2.3 The amount, tissue location and composition -
Maize (Zea Mays L.) Nucleoskeletal Proteins Regulate Nuclear Envelope 2 Remodeling and Function in Stomatal Complex Development and Pollen Viability
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.23.424208; this version posted December 24, 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 Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope 2 remodeling and function in stomatal complex development and pollen viability. 3 McKenna JF*✝, Gumber HK*, Turpin ZM, Jalovec AM, Kartick AC, Graumann K#, and 4 Bass HW# 5 *co-first authors, equal contributions 6 # co-corresponding authors 7 8 email addresses: 9 10 Joseph F. McKenna, [email protected], Department of Biological and 11 Medical Sciences, Oxford Brookes University, Oxford, UK 12 ✝ Current address: [email protected], School of Life Sciences, University 13 of Warwick, Coventry, CV4 7AL, UK, ORCID 0000-0003-4838-6048 14 15 Hardeep K. Gumber, [email protected], Department of Biological Science, Florida 16 State University, Tallahassee, FL, USA, ORCID 0000-0001-5250-7207 17 18 Zachary M. Turpin, [email protected], Department of Biological Science, Florida State 19 University, Tallahassee, FL, USA 20 21 Alexis M. Jalovec, [email protected], Department of Biological Science, Florida State 22 University, Tallahassee, FL, USA 23 24 Andre C. Kartick, [email protected], Department of Biological Science, Florida State 25 University, Tallahassee, FL, USA 26 Katja Graumann, [email protected], Department of Biological and Medical 27 Sciences, Oxford Brookes University, Oxford, UK 28 Hank W. -
The Hybrid Motor in Shewanella Oneidensis MR-1
Flagellar motor tuning The hybrid motor in Shewanella oneidensis MR-1 Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) dem Fachbereich Biologie der Philipps-Universität Marburg vorgelegt von Anja Paulick aus Hoyerswerda Marburg (Lahn), 2012 Die Untersuchungen zur vorliegenden Arbeit wurden von Mai 2008 bis März 2012 am Max-Planck-Institut für terrestrische Mikrobiologie unter der Leitung von Dr. Kai M. Thormann durchgeführt. Vom Fachbereich Biologie der Philipps-Universität Marburg (HKZ: 1180) als Dissertation angenommen am: 03.04.2012 Erstgutachter: Dr. Kai M. Thormann Zweitgutachter: Prof. Dr. Martin Thanbichler Weitere Mitglieder der Prüfungskommission: Prof. Dr. Klaus Lingelbach Prof. Dr. Uwe G. Maier Prof. Dr. Alexander Böhm Tag der mündlichen Prüfung: 06.09.2012 Die während der Promotion erzielten Ergebnisse sind zum Teil in folgenden Originalpublikationen veröffentlicht: Paulick A, Koerdt A, Lassak J, Huntley S, Wilms I, Narberhaus F, Thormann KM: Two different stator systems drive a single polar flagellum in Shewanella oneidensis MR-1. Mol Microbiol 2009, 71:836-850. Koerdt A1, Paulick A1, Mock M, Jost K, Thormann KM: MotX and MotY are required for flagellar rotation in Shewanella oneidensis MR-1. J Bacteriol 2009, 191:5085-5093. Thormann KM, Paulick A: Tuning the flagellar motor. Microbiology 2010, 156:1275-1283. Ergebnisse aus in dieser Promotion nicht erwähnten Projekten sind in folgenden Originalpublikationen veröffentlicht: Bubendorfer S, Held S, Windel N, Paulick A, Klingl A, Thormann KM: Specificity of motor components in the dual flagellar system of Shewanella putrefaciens CN-32. Mol Microbiol 2011. 1 diese Autoren wirkten gleichberechtigt an der Publikation mit Ich versichere, dass ich meine Dissertation: “Flagellar motor tuning The hybrid motor in Shewanella oneidensis MR-1” selbstständig, ohne unerlaubte Hilfe angefertigt und mich dabei keiner anderen als der von mir ausdrücklich bezeichneten Quellen und Hilfen bedient habe. -
Evolutionary Genomics of a Plastic Life History Trait: Galaxias Maculatus Amphidromous and Resident Populations
EVOLUTIONARY GENOMICS OF A PLASTIC LIFE HISTORY TRAIT: GALAXIAS MACULATUS AMPHIDROMOUS AND RESIDENT POPULATIONS by María Lisette Delgado Aquije Submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at Dalhousie University Halifax, Nova Scotia August 2021 Dalhousie University is located in Mi'kma'ki, the ancestral and unceded territory of the Mi'kmaq. We are all Treaty people. © Copyright by María Lisette Delgado Aquije, 2021 I dedicate this work to my parents, María and José, my brothers JR and Eduardo for their unconditional love and support and for always encouraging me to pursue my dreams, and to my grandparents Victoria, Estela, Jesús, and Pepe whose example of perseverance and hard work allowed me to reach this point. ii TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ........................................................................................................... ix ABSTRACT ...................................................................................................................... xii LIST OF ABBREVIATION USED ................................................................................ xiii ACKNOWLEDGMENTS ................................................................................................ xv CHAPTER 1. INTRODUCTION ....................................................................................... 1 1.1 Galaxias maculatus .................................................................................................. -
Thesis Was Carried out at the Centre for Geobiology and Department of Biology at the University of Bergen
The Arctic Mid-Ocean Ridge Vent Fields – A valuable Resource for Marine Bioprospecting? Juliane Wissuwa Dissertation for the degree of philosophiae doctor (PhD) at the University of Bergen 2016 Dissertation date: May 25th 2016 © Copyright Juliane Wissuwa The material in this publication is protected by copyright law. Year: 2016 Title: The Arctic Mid-Ocean Ridge Vent Fields – A valuable Resource for Marine Bioprospecting? Author: Juliane Wissuwa Print: AiT Bjerch AS / University of Bergen ŝŝŝ Contents Scientific environment .............................................................................................................. v Acknowledgements .................................................................................................................. vi Abstract .................................................................................................................................. viii Abbreviations ............................................................................................................................ x List of Publications .................................................................................................................. xi 1. Introduction ....................................................................................................................... 1 1.1 Background ................................................................................................................ 1 1.2 Enzymes from extremophiles and their biotechnological application ...................... -
Thèse Morgane Wartel
Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. Tâm Mignot Directeur de Thèse Pr. Frédéric Barras Président du Jury Faculté des Sciences - Aix-Marseille Université Laboratoire de Chimie Bactérienne 163 Avenue de Luminy - Case 901 31 Chemin Joseph Aiguier 13288 Marseille 13009 Marseille Thèse En vue d’obtenir le grade de Docteur d’Aix-Marseille Université Biologie, spécialité Microbiologie Présentée et soutenue publiquement par Morgane Wartel Le Mercredi 18 Décembre 2013 A novel class of bacterial motors involved in the directional transport of a sugar at the bacterial surface: The machineries of motility and sporulation in Myxococcus xanthus. Une nouvelle classe de moteurs bactériens impliqués dans le transport de macromolécules à la surface bactérienne: Les machineries de motilité et de sporulation de Myxococcus xanthus. Membres du Jury : Dr. Christophe Grangeasse Rapporteur Dr. Patrick Viollier Rapporteur Pr. Pascale Cossart Examinateur Dr. Francis-André Wollman Examinateur Dr. -
Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database. -
Influence of Post-Anthesis Drought Stress on Germination and Malting Quality in Barley
Influence of post-anthesis drought stress on germination and malting quality in barley Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften (Dr. rer. nat.) der Naturwissenschaftlichen Fakultät – Biowissenschaften – der Martin-Luther-Universität Halle-Wittenberg vorgelegt von Korana Surdonja geb. am: 17.04.1986 in: Koper, Slowenien Gutachter: 1. Prof. Dr. Thomas Altmann 2. Prof. Dr. Klaus Humbeck 3. Prof. Dr. Wolfgang Dröge-Laser Datum der Verteidigung: 06.03.2019 Contents List of figures ............................................................................................................................... i List of tables ............................................................................................................................... iii Abbreviation ........................................................................................................................... iv 1 Introduction .............................................................................................................................. 1 1.1 Characteristics of malting barley grain .............................................................................. 1 Endosperm ........................................................................................................................... 2 Aleurone layer ..................................................................................................................... 5 Embryo ............................................................................................................................... -
Life in the Cold Biosphere: the Ecology of Psychrophile
Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole. -
Pseudidiomarina Taiwanensis Gen. Nov., Sp. Nov., a Marine Bacterium
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 899–905 DOI 10.1099/ijs.0.64048-0 Pseudidiomarina taiwanensis gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water of An-Ping Harbour, Taiwan, and emended description of the family Idiomarinaceae Wen Dar Jean,1 Wung Yang Shieh2 and Hsiu-Hui Chiu2 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Rd, Tainan, Wung Yang Shieh Taiwan [email protected] 2Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan Two strains of heterotrophic, aerobic, marine bacteria, designated strains PIT1T and PIT2, were isolated from sea-water samples collected at the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Both strains were Gram-negative. Cells grown in broth cultures were straight rods that were non-motile, lacking flagella. Both strains required NaCl for growth and exhibited optimal growth at 30–35 6C, 1–4 % NaCl and pH 8. They grew aerobically and were incapable of anaerobic growth by fermentation of glucose or other carbohydrates. Cellular fatty acids were predominantly iso-branched, with C15 : 0 iso and C17 : 0 iso representing the most abundant components. The DNA G+C contents of strains PIT1T and PIT2 were 49?3 and 48?6 mol%, respectively. Phylogeny based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that the two isolates could be assigned to a novel genus in the family Idiomarinaceae, for which the name Pseudidiomarina gen. nov. is proposed. Pseudidiomarina taiwanensis sp. nov. is the type species of the novel genus (type strain PIT1T=BCRC 17465T=JCM 13360T). -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments.