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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. -
Inferring Gene Function from Evolutionary Change in Signatures
Krisko et al. Genome Biology 2014, 15:R44 http://genomebiology.com/2014/15/3/R44 RESEARCH Open Access Inferring gene function from evolutionary change in signatures of translation efficiency Anita Krisko1, Tea Copic1, Toni Gabaldón2,3,5, Ben Lehner3,4,5 and Fran Supek2,3,4* Abstract Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results: Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13/15, 19/23, and 3/6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H. Conclusions: Taken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. -
Bacterium That Produces Antifouling Agents
International Journal of Systematic Bacteriology (1998), 48, 1205-1 21 2 Printed in Great Britain ~- Pseudoalteromonas tunicata sp. now, a bacterium that produces antifouling agents Carola Holmstromfl Sally James,’ Brett A. Neilan,’ David C. White’ and Staffan Kjellebergl Author for correspondence : Carola Holmstrom. Tel: + 61 2 9385 260 1. Fax: + 6 1 2 9385 159 1. e-mail: c.holmstrom(cx unsw.edu.au 1 School of Microbiology A dark-green-pigmented marine bacterium, previously designated D2, which and Immunology, The produces components that are inhibitory to common marine fouling organisms University of New South Wales, Sydney 2052, has been characterized and assessed for taxonomic assignment. Based on Australia direct double-stranded sequencing of the 16s rRNA gene, D2Twas found to show the highest similarity to members of the genus 2 Center for Environmental (93%) B iotechnology, Un iversity Pseudoalteromonas. The G+C content of DZT is 42 molo/o, and it is a of Tennessee, 10515 facultatively anaerobic rod and oxidase-positive. DZT is motile by a sheathed research Drive, Suite 300, Knoxville, TN 37932, USA polar flagellum, exhibited non-fermentative metabolism and required sodium ions for growth. The strain was not capable of using citrate, fructose, sucrose, sorbitol and glycerol but it utilizes mannose and maltose and hydrolyses gelatin. The molecular evidence, together with phenotypic characteristics, showed that this bacterium which produces an antifouling agent constitutes a new species of the genus Pseudoalteromonas.The name Pseudoalteromonas tunicata is proposed for this bacterium, and the type strain is DZT (= CCUG 2 6 7 5 7T). 1 Kevwords: PseudoalttJvomonas tunicata, pigment, antifouling bacterium, marine, 16s I rRNA sequence .__ , INTRODUCTION results suggested that the genus Alteromonas should be separated into two genera. -
Genomic and Phenotypic Insights Into the Ecology of Arthrobacter from Antarctic Soils Melissa Dsouza1*, Michael W Taylor1, Susan J Turner1,2 and Jackie Aislabie3
Dsouza et al. BMC Genomics (2015) 16:36 DOI 10.1186/s12864-015-1220-2 RESEARCH ARTICLE Open Access Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils Melissa Dsouza1*, Michael W Taylor1, Susan J Turner1,2 and Jackie Aislabie3 Abstract Background: Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. Results: Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. -
1 Large-Scale Maps of Variable Infection Efficiencies in Aquatic Bacteroidetes Phage
1 Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage- 2 host model systems 3 Karin Holmfeldt1,2, Natalie Solonenko1,a, Cristina Howard-Varona1,a, Mario Moreno1, 4 Rex R. Malmstrom3, Matthew J. Blow3, Matthew B. Sullivan1,a,b 5 1Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 6 USA 7 2Centre for Ecology and Evolution in Microbial Model Systems, Department of Biology 8 and Environmental Sciences, Linnaeus University, Kalmar, Sweden 9 3DOE Joint Genome Institute, Walnut Creek, CA, USA 10 Current affiliation: Departments of aMicrobiology, and bCivil, Environmental and 11 Geodetic Engineering, The Ohio State University, Columbus, OH 12 * corresponding author: Karin Holmfeldt, Center for Ecology and Evolution in Microbial 13 Model Systems, Department of Biology and Environmental Sciences, Linnaeus 14 University, SE-391 82 Kalmar, Sweden. Phone nr +46-480-447310, Fax nr +46-480- 15 447305, email [email protected]. 16 17 Running title: Variable phage-host infection interactions 1 18 Summary 19 Microbes drive ecosystem functioning, and their viruses modulate these impacts through 20 mortality, gene transfer, and metabolic reprogramming. Despite the importance of virus- 21 host interactions and likely variable infection efficiencies of individual phages across 22 hosts, such variability is seldom quantified. Here we quantify infection efficiencies of 38 23 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model 24 systems. Binary data revealed that some phages infected only one strain while others 25 infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 26 orders of magnitude, even among phages within one population. -
Targeting of Flavobacterium Johnsoniae Proteins for Secretion by the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee
University of Wisconsin Milwaukee UWM Digital Commons Theses and Dissertations May 2017 Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System Surashree Sunil Kulkarni University of Wisconsin-Milwaukee Follow this and additional works at: https://dc.uwm.edu/etd Part of the Microbiology Commons Recommended Citation Kulkarni, Surashree Sunil, "Targeting of Flavobacterium Johnsoniae Proteins for Secretion By the Type IX Secretion System" (2017). Theses and Dissertations. 1501. https://dc.uwm.edu/etd/1501 This Dissertation is brought to you for free and open access by UWM Digital Commons. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of UWM Digital Commons. For more information, please contact [email protected]. TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biological Sciences at The University of Wisconsin-Milwaukee May 2017 ABSTRACT TARGETING OF FLAVOBACTERIUM JOHNSONIAE PROTEINS FOR SECRETION BY THE TYPE IX SECRETION SYSTEM by Surashree S. Kulkarni The University of Wisconsin-Milwaukee, 2017 Under the Supervision of Dr. Mark J. McBride Flavobacterium johnsoniae and many related bacteria secrete proteins across the outer membrane using the type IX secretion system (T9SS). Proteins secreted by T9SSs have amino-terminal signal peptides for export across the cytoplasmic membrane by the Sec system and carboxy-terminal domains (CTDs) targeting them for secretion across the outer membrane by the T9SS. Most but not all T9SS CTDs belong to family TIGR04183 (type A CTDs). -
Extreme Cold Environments: a Suitable Niche for Selection of Novel Psychrotrophic Microbes for Biotechnological Applications
Editorial Adv Biotech & Micro Volume 2 Issue 2 - February 2017 Copyright © All rights are reserved by Ajar Nath Yadav DOI: 10.19080/AIBM.2017.02.555584 Extreme Cold Environments: A Suitable Niche for Selection of Novel Psychrotrophic Microbes for Biotechnological Applications Ajar Nath Yadav1*, Priyanka Verma2, Vinod Kumar1, Shashwati Ghosh Sachan3 and Anil Kumar Saxena4 1Department of Biotechnology, Eternal University, India 2Department of Microbiology, Eternal University, India 3Department of Bio-Engineering, Birla Institute of Technology, India 4ICAR-National Bureau of Agriculturally Important Microorganisms, India Submission: January 27, 2017; Published: February 06, 2017 *Corresponding author: Ajar Nath Yadav, Assistant professor, Department of Biotechnology, Akal College of Agriculture, Eternal University, India, Tel: ; Email: Editorial several reports on whole genome sequences of novel and The microbiomes of cold environments are of particular potential psychrotrophic microbes [26,27]. importance in global ecology since the majority of terrestrial and aquatic ecosystems of our planet are permanently or The novel species of psychrotrophic microbes have been seasonally submitted to cold temperatures. Earth is primarily a isolated worldwide and reported from different domain cold, marine planet with 90% of the ocean’s waters being at 5°C archaea, bacteria and fungi which included members of phylum or lower. Permafrost soils, glaciers, polar sea ice, and snow cover Actinobacteria, Proteobacteria, Bacteroidetes, Basidiomycota, make up 20% of the Earth’s surface environments. Microbial Firmicutes and Euryarchaeota [7-25]. Along with novel species communities under cold habitats have been undergone the of psychrotrophic microbes, some microbial species including physiological adaptations to low temperature and chemical Arthrobacter nicotianae, Brevundimonas terrae, Paenibacillus stress. -
University of Copenhagen
Identification and Characterization of a -N-Acetylhexosaminidase with a Biosynthetic Activity from the Marine Bacterium Paraglaciecola hydrolytica S66T Visnapuu, Triinu; Teze, David; Kjeldsen, Christian; Lie, Aleksander; Duus, Jens Øllgaard; André-Miral, Corinne; Pedersen, Lars Haastrup; Stougaard, Peter; Svensson, Birte Published in: International Journal of Molecular Sciences DOI: 10.3390/ijms21020417 Publication date: 2020 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Visnapuu, T., Teze, D., Kjeldsen, C., Lie, A., Duus, J. Ø., André-Miral, C., ... Svensson, B. (2020). Identification and Characterization of a -N-AcetylhexosaminidaseT with a Biosynthetic Activity from the Marine Bacterium Paraglaciecola hydrolytica S66 . International Journal of Molecular Sciences, 21(2). https://doi.org/10.3390/ijms21020417 Download date: 23. Jun. 2020 International Journal of Molecular Sciences Article Identification and Characterization of a β-N-Acetylhexosaminidase with a Biosynthetic Activity from the Marine Bacterium Paraglaciecola hydrolytica S66T 1,2, 1 3 4, Triinu Visnapuu * , David Teze , Christian Kjeldsen , Aleksander Lie y , 3 5 4 6, Jens Øllgaard Duus , Corinne André-Miral , Lars Haastrup Pedersen , Peter Stougaard z and Birte Svensson 1,* 1 Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark; [email protected] 2 Institute of Molecular and Cell Biology, University of Tartu, -
Genomic and Phenotypic Analyses of Chitin Degradation and Secondary Metabolite Production in Pseudoalteromonas
Downloaded from orbit.dtu.dk on: Oct 06, 2021 Genomic and phenotypic analyses of chitin degradation and secondary metabolite production in Pseudoalteromonas Paulsen, Sara Skøtt Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Paulsen, S. S. (2020). Genomic and phenotypic analyses of chitin degradation and secondary metabolite production in Pseudoalteromonas. DTU Bioengineering. 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 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. Genomic and phenotypic analyses of chitin degradation and secondary metabolite production in Pseudoalteromonas Sara Skøtt Paulsen PhD Thesis March 2020 Preface This present PhD study serves as a partial fulfillment of the requirements to obtain a PhD degree from the Technical University of Denmark (DTU). The work has has been carried out at the Department of Biotechnology and Biomedicine (DTU Bioengineering) from October 2016 to March 2020 under the supervision of Professor Lone Gram and Senior Researcher Eva Sonnenschein. -
The Bacterial Basis of Biofouling: a Case Study
Indian Journal of Geo-Marine Sciences Vol. 43(11), November 2014, pp. 2075-2084 The Bacterial Basis of Biofouling: a Case Study Michael G. Hadfield*, Audrey Asahina, Shaun Hennings and Brian Nedved Kewalo Marine Laboratory, University of Hawaii at Manoa 41 Ahui St., Honolulu, Hawaii, 96813 USA *[E-mail: [email protected]] Received 07 March 2014; revised 14 September 2014 For billions of years bacteria have profusely colonized all parts of the oceans and formed biofilms on the benthos. Thus, from their onset, evolving marine animals adapted to the microbial world throughout their life cycles. One of the major adaptations is the use of bacterial products as signals for recruitment by larvae of many species in the seven invertebrate phyla that make up most of the biofouling community. We describe here investigations on the recruitment biology of one such species, the circum-tropical serpulid polychaete Hydroides elegans. Insights gained from in-depth studies on adults and larvae of H. elegans include: apparently constant transport of these biofouling worms on the hulls of ships maintains a globally panmictic population; larvae complete metamorphosis with little or no de novo gene transcription or translation; larvae of this tube-worm settle selectively in response to specific biofilm-dwelling bacterial species; and biofilms provide not only a cue for settlement sites, but also increase the adhesion strength of the settling worms’ tubes on a substratum. Although biofilm-bacterial species are critical to larval-settlement induction, not all biofilm elements are inductive. Because studies on chemoreception systems in the larvae failed to find evidence for the presence of common chemoreceptors, we focused on the bacterial cues themselves. -
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. -
Ichthyenterobacterium Magnum.Pdf
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1186–1192 DOI 10.1099/ijs.0.000078 Ichthyenterobacterium magnum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from olive flounder (Paralichthys olivaceus) Qismat Shakeela, Ahmed Shehzad, Kaihao Tang, Yunhui Zhang and Xiao-Hua Zhang Correspondence College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China Xiao-Hua Zhang [email protected] A novel marine bacterium isolated from the intestine of cultured flounder (Paralichthys olivaceus) was studied by using a polyphasic taxonomic approach. The isolate was Gram-stain-negative, pleomorphic, aerobic, yellow and oxidase- and catalase-negative. Phylogenetic analysis of 16S rRNA gene sequences indicated that isolate Th6T formed a distinct branch within the family Flavobacteriaceae and showed 96.6 % similarity to its closest relative, Bizionia hallyeonensis T- y7T. The DNA G+C content was 29 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C15 : 1 G, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C15 : 1v6c and/or C16 : 1v7c). On the basis of the phenotypic, chemotaxo- nomic and phylogenetic characteristics, the novel bacterium has been assigned to a novel species of a new genus for which the name Ichthyenterobacterium magnum gen. nov., sp. nov. is proposed. The type strain is Th6T (5JCM 18636T5KCTC 32140T). The family Flavobacteriaceae was proposed by Jooste sampled aseptically by dissecting the fish. Th6T was isolated (1985) and was included in the first edition of Bergey’s from the tissue homogenate by the plate spreading method Manual of Systematic Bacteriology (Reichenbach, 1989).