Coal-Miner: a Statistical Method for GWA Studies of !Antitative Traits with Complex Evolutionary Origins
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Iron Transport Strategies of the Genus Burkholderia
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2015 Iron transport strategies of the genus Burkholderia Mathew, Anugraha Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-113412 Dissertation Published Version Originally published at: Mathew, Anugraha. Iron transport strategies of the genus Burkholderia. 2015, University of Zurich, Faculty of Science. Iron transport strategies of the genus Burkholderia Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftlichen Fakultät der Universität Zürich von Anugraha Mathew aus Indien Promotionskomitee Prof. Dr. Leo Eberl (Vorsitz) Prof. Dr. Jakob Pernthaler Dr. Aurelien carlier Zürich, 2015 2 Table of Contents Summary .............................................................................................................. 7 Zusammenfassung ................................................................................................ 9 Abbreviations ..................................................................................................... 11 Chapter 1: Introduction ....................................................................................... 14 1.1.Role and properties of iron in bacteria ...................................................................... 14 1.2.Iron transport mechanisms in bacteria ..................................................................... -
Broad-Spectrum Antimicrobial Activity by Burkholderia Cenocepacia Tatl-371, a Strain Isolated from the Tomato Rhizosphere
RESEARCH ARTICLE Rojas-Rojas et al., Microbiology DOI 10.1099/mic.0.000675 Broad-spectrum antimicrobial activity by Burkholderia cenocepacia TAtl-371, a strain isolated from the tomato rhizosphere Fernando Uriel Rojas-Rojas,1 Anuar Salazar-Gómez,1 María Elena Vargas-Díaz,1 María Soledad Vasquez-Murrieta, 1 Ann M. Hirsch,2,3 Rene De Mot,4 Maarten G. K. Ghequire,4 J. Antonio Ibarra1,* and Paulina Estrada-de los Santos1,* Abstract The Burkholderia cepacia complex (Bcc) comprises a group of 24 species, many of which are opportunistic pathogens of immunocompromised patients and also are widely distributed in agricultural soils. Several Bcc strains synthesize strain- specific antagonistic compounds. In this study, the broad killing activity of B. cenocepacia TAtl-371, a Bcc strain isolated from the tomato rhizosphere, was characterized. This strain exhibits a remarkable antagonism against bacteria, yeast and fungi including other Bcc strains, multidrug-resistant human pathogens and plant pathogens. Genome analysis of strain TAtl-371 revealed several genes involved in the production of antagonistic compounds: siderophores, bacteriocins and hydrolytic enzymes. In pursuit of these activities, we observed growth inhibition of Candida glabrata and Paraburkholderia phenazinium that was dependent on the iron concentration in the medium, suggesting the involvement of siderophores. This strain also produces a previously described lectin-like bacteriocin (LlpA88) and here this was shown to inhibit only Bcc strains but no other bacteria. Moreover, a compound with an m/z 391.2845 with antagonistic activity against Tatumella terrea SHS 2008T was isolated from the TAtl-371 culture supernatant. This strain also contains a phage-tail-like bacteriocin (tailocin) and two chitinases, but the activity of these compounds was not detected. -
Molecular Study of the Burkholderia Cenocepacia Division Cell Wall Operon and Ftsz Interactome As Targets for New Drugs
Università degli Studi di Pavia Dipartimento di Biologia e Biotecnologie “L. Spallanzani” Molecular study of the Burkholderia cenocepacia division cell wall operon and FtsZ interactome as targets for new drugs Gabriele Trespidi Dottorato di Ricerca in Genetica, Biologia Molecolare e Cellulare XXXIII Ciclo – A.A. 2017-2020 Università degli Studi di Pavia Dipartimento di Biologia e Biotecnologie “L. Spallanzani” Molecular study of the Burkholderia cenocepacia division cell wall operon and FtsZ interactome as targets for new drugs Gabriele Trespidi Supervised by Prof. Edda De Rossi Dottorato di Ricerca in Genetica, Biologia Molecolare e Cellulare XXXIII Ciclo – A.A. 2017-2020 Cover image: representation of the Escherichia coli division machinery. Created by Ornella Trespidi A tutta la mia famiglia e in particolare a Diletta Table of contents Abstract ..................................................................................................... 1 Abbreviations ............................................................................................ 3 1. Introduction ........................................................................................... 5 1.1 Cystic fibrosis 5 1.1.1 CFTR defects in CF 5 1.1.2 Pathophysiology of CF 7 1.1.3 CFTR modulator therapies 11 1.2 CF-associated lung infections 12 1.2.1 Pseudomonas aeruginosa 13 1.2.2 Staphylococcus aureus 14 1.2.3 Stenotrophomonas maltophilia 15 1.2.4 Achromobacter xylosoxidans 16 1.2.5 Non-tuberculous mycobacteria 17 1.3 The genus Burkholderia 18 1.3.1 Burkholderia cepacia complex 20 1.3.2 Bcc species as CF pathogens 22 1.4 Burkholderia cenocepacia 23 1.4.1 B. cenocepacia epidemiology 23 1.4.2 B. cenocepacia genome 25 1.4.3 B. cenocepacia pathogenicity and virulence factors 26 1.4.3.1 Quorum sensing 29 1.4.3.2 Biofilm 32 1.4.4 B. -
Clinical Outcome of Burkholderia Cepacia Complex Infection in Cystic Fibrosis Adults$
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Journal of Cystic Fibrosis 3 (2004) 93–98 www.elsevier.com/locate/jcf Clinical outcome of Burkholderia cepacia complex infection in cystic fibrosis adults$ J.M. Courtneya,b, K.E.A. Dunbarb,c, A. McDowellc, J.E. Moorec, T.J. Warkea,b, M. Stevensond, J.S. Elborna,b,* a Adult Cystic Fibrosis Centre, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, North Ireland, UK b Centre for Inflammation, Queens University, Belfast, UK c Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, UK d Department of Medical Statistics, Queens University, Belfast, UK Received 2 January 2003; accepted 28 January 2004 Available online Abstract Background: The Burkholderia cepacia complex (BCC) is one of the most important groups of organisms infecting cystic fibrosis (CF) patients. The aim of the study was to examine how infection with BCC affects clinical outcome. Methods: Nineteen CF adults infected with BCC and 19 controls infected with Pseudomonas aeruginosa were studied over a 4-year period. The best forced expiratory volume in 1 s (FEV1) and body mass index (BMI) for each year were recorded and annual rate of decline calculated. Results: The BCC infected group displayed a significantly greater reduction of FEV1 and BMI compared to the P. aeruginosa infected group ( p = 0.001 and p = 0.009, respectively). Sixteen patients infected with a single Burkholderia cenocepacia strain had a significantly greater rate of FEV1 decline compared to those infected with Burkholderia multivorans (n =3)orP. -
Material and Methods
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2011 Investigations of the Quorum sensing circuitry in ”Burkholderia cenocepacia” H111 Inhülsen, Silja Abstract: Burkholderia cenocepacia ist ein Gram-negatives Bakterium, welches ubiquitär in der Umwelt vorkommt. Vor drei Jahrzehnten wurde B. cenocepacia als verursachender Erreger von schwerwiegen- den Lungenentzündungen in Patienten mit zystischer Fibrose (CF) identifiziert. Die Infektionen waren von einer charakteristischen Bakteriämie gekennzeichnet und führten zum frühen Tod der CF-Kranken. Seither wurde B. cenocepacia als ein zunehmend problematisches opportunistisches Pathogen in immun- supprimierten Individuen wahrgenommen, welches die Notwendigkeit für die weitere Erforschung und Aufklärung von Virulenzfaktoren von B. cenocepacia begründet. Es wurde aufgezeigt, dass die Aus- bildung von pathogenen Eigenschaften in B. cenocepacia entscheidend durch „Quorum sensing“ (QS) beeinflusst wird, welches vor allem duch das CepIR-Regulationssystem vermittelt wird, das die Expres- sion bestimmter Gene in Abhängigkeit von der Populationsdichte kontrolliert. In der vorliegenden Arbeit wurde das QS-Regulon von B. cenocepacia H111 entschlüsselt und detalliert analysiert. Die Identifizierung von CepIR-regulierten Funktionen gelang dabei durch die Implementierung einer kombinierten transkrip- tionellen, proteomischen und phänotypischen Herangehensweise. Die Ergebnisse dieser Analyse liefern neue Erkenntnisse über im Vorfeld -
The Human Immune Response to the Flagellins of Burkholderia Dolosa
University of Louisville ThinkIR: The University of Louisville's Institutional Repository College of Arts & Sciences Senior Honors Theses College of Arts & Sciences 5-2014 The human immune response to the flagellins of Burkholderia dolosa. Molly McDonald University of Louisville Follow this and additional works at: https://ir.library.louisville.edu/honors Part of the Biology Commons Recommended Citation McDonald, Molly, "The human immune response to the flagellins of Burkholderia dolosa." (2014). College of Arts & Sciences Senior Honors Theses. Paper 82. http://doi.org/10.18297/honors/82 This Senior Honors Thesis is brought to you for free and open access by the College of Arts & Sciences at ThinkIR: The University of Louisville's Institutional Repository. It has been accepted for inclusion in College of Arts & Sciences Senior Honors Theses by an authorized administrator of ThinkIR: The University of Louisville's Institutional Repository. This title appears here courtesy of the author, who has retained all other copyrights. For more information, please contact [email protected]. The Human Immune Response to the Flagellins of Burkholderia dolosa By Molly McDonald Submitted in partial fulfillment of the requirements for Graduation summa cum laude and for Graduation with Honors from the Department of Biology University of Louisville May 2014 Table of Contents Abstract .......................................................................................................................................... 4 Introduction .................................................................................................................................. -
Tangled Bank of Experimentally Evolved Burkholderia Biofilms
Tangled bank of experimentally evolved Burkholderia PNAS PLUS biofilms reflects selection during chronic infections Charles C. Traverse, Leslie M. Mayo-Smith, Steffen R. Poltak, and Vaughn S. Cooper1 Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824 Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved November 29, 2012 (received for review April 26, 2012) How diversity evolves and persists in biofilms is essential for Although this species has been identified as the most prevalent and understanding much of microbial life, including the uncertain pathogenic of the Burkholderia cepacia complex species in CF dynamics of chronic infections. We developed a biofilm model patients (14), relatively little is known about how it adapts to enabling long-term selection for daily adherence to and dispersal a biofilm lifestyle or to the CF lung environment (5, 16). from a plastic bead in a test tube. Focusing on a pathogen of the Six B. cenocepacia populations underwent ∼1,050 generations cystic fibrosis lung, Burkholderia cenocepacia, we sequenced of biofilm selection, all of which diversified into similar sets of clones and metagenomes to unravel the mutations and evolution- three distinct, heritable colony morphotypes from a single an- ary forces responsible for adaptation and diversification of a single cestral clone (Fig. 1) (4). At least one of these morphotypes— biofilm community during 1,050 generations of selection. The mu- a small, highly rugose “wrinkly” type (17)—is commonly isolated tational patterns revealed recurrent evolution of biofilm specialists from chronic lung infections of both Burkholderia spp. and from generalist types and multiple adaptive alleles at relatively few Pseudomonas aeruginosa and has been associated with high pa- loci. -
Burkholderia Sigma Factor Systems with Metal-Responsive Regulatory Domains
Burkholderia sigma factor systems with metal-responsive regulatory domains By: Christopher D. Banyard A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy The University of Sheffield Faculty of Medicine, Dentistry and Health, The Medical School Department of Infection, Immunity and Cardiovascular Disease Submission Date: October 2019 Acknowledgments I owe a great deal to my supervisor Dr Mark Thomas for his patience, support and guidance over the years. I would also like to thank Professor Jeff Green, for his valuable insights and encouragement. I am indebted to Dr Srdjan (Guta) Vitovski for his work and training in performing bio layer interferometry assays. I am also grateful to the BBSRC White Rose Mechanistic Biology DTP for funding this project. There are many members of lab LU103 whom I am thankful to have worked with, and you all made the many hours spending toiling away more bearable. I am especially grateful to Dr Aaron Butt – he paved the way forward for my work and taught me everything from how to perform a β-gal assay to where the best lunch could be found (I miss our Falafel King Fridays!). I would like to thank the wider Infection, Immunity and Cardiovascular Disease department for providing all the training and resources that made this work possible. I will be eternally grateful to all the family and friends who have supported me along the way, maybe without even realising it. I will always remember your confidence in me, when I had none. I am especially grateful to my parents, for their guidance and trust for as long as I can remember. -
Research Article Burkholderia Contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes
Hindawi Publishing Corporation BioMed Research International Volume 2016, Article ID 6560534, 13 pages http://dx.doi.org/10.1155/2016/6560534 Research Article Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes Olga L. Voronina,1 Marina S. Kunda,1 Natalia N. Ryzhova,1 Ekaterina I. Aksenova,1 Andrey N. Semenov,1 Yulia M. Romanova,1,2 and Alexandr L. Gintsburg1,2 1 N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russia, Gamaleya Street 18, Moscow 123098, Russia 2I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia Correspondence should be addressed to Olga L. Voronina; [email protected] Received 24 February 2016; Accepted 8 November 2016 Academic Editor: Vassily Lyubetsky Copyright © 2016 Olga L. Voronina et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Biofilm formation by Burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. A “lacking biofilm production” (LBP) strain B. contaminans GIMC4587:Bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. It has an interrupted transcriptional response regulator (RR) gene. The focus of our investigation was a two-component signal transduction system determination, including this RR. B. contaminans clinical and LBP strains were analyzed by whole genome sequencing and bioinformatics resources. A four-component operon (BiofilmReg) has a key role in biofilm formation. The relative location (i.e., by being separated by another gene) of RR and histidine kinase genes is uniquein BiofilmReg. -
Burkholderia Bacteria Produce Multiple Potentially Novel Molecules That Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens
antibiotics Article Burkholderia Bacteria Produce Multiple Potentially Novel Molecules that Inhibit Carbapenem-Resistant Gram-Negative Bacterial Pathogens Eliza Depoorter 1 , Evelien De Canck 1, Tom Coenye 2 and Peter Vandamme 1,* 1 Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium; [email protected] (E.D.); [email protected] (E.D.C.) 2 Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Ghent University, 9000 Ghent, Belgium; [email protected] * Correspondence: [email protected]; Tel.: +32-9264-5113 Abstract: Antimicrobial resistance in Gram-negative pathogens represents a global threat to human health. This study determines the antimicrobial potential of a taxonomically and geographically diverse collection of 263 Burkholderia (sensu lato) isolates and applies natural product dereplication strategies to identify potentially novel molecules. Antimicrobial activity is almost exclusively present in Burkholderia sensu stricto bacteria and rarely observed in the novel genera Paraburkholderia, Caballero- nia, Robbsia, Trinickia, and Mycetohabitans. Fourteen isolates show a unique spectrum of antimicrobial activity and inhibited carbapenem-resistant Gram-negative bacterial pathogens. Dereplication of the molecules present in crude spent agar extracts identifies 42 specialized metabolites, 19 of which repre- sented potentially novel molecules. The known identified Burkholderia metabolites include toxoflavin, reumycin, pyrrolnitrin, -
Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis
Curr Microbiol DOI 10.1007/s00284-013-0330-9 Phylogenetic Analysis of Burkholderia Species by Multilocus Sequence Analysis Paulina Estrada-de los Santos • Pablo Vinuesa • Lourdes Martı´nez-Aguilar • Ann M. Hirsch • Jesu´s Caballero-Mellado Received: 11 August 2012 / Accepted: 21 January 2013 Ó Springer Science+Business Media New York 2013 Abstract Burkholderia comprises more than 60 species bacterial species. The group B comprises the B. cepacia of environmental, clinical, and agro-biotechnological rel- complex (opportunistic human pathogens), the B. pseudo- evance. Previous phylogenetic analyses of 16S rRNA, mallei subgroup, which includes both human and animal recA, gyrB, rpoB, and acdS gene sequences as well as pathogens, and an assemblage of plant pathogenic species. genome sequence comparisons of different Burkholderia The distinct lineages present in Burkholderia suggest that species have revealed two major species clusters. In this each group might represent a different genus. However, it study, we undertook a multilocus sequence analysis of 77 will be necessary to analyze the full set of Burkholderia type and reference strains of Burkholderia using atpD, species and explore whether enough phenotypic features gltB, lepA, and recA genes in combination with the 16S exist among the different clusters to propose that these rRNA gene sequence and employed maximum likelihood groups should be considered separate genera. and neighbor-joining criteria to test this further. The phy- logenetic analysis revealed, with high supporting values, Abbreviations distinct lineages within the genus Burkholderia. The two MLSA Multilocus sequence analysis large groups were named A and B, whereas the B. rhi- BCC Burkholderia cepacia complex zoxinica/B. -
Genomic Phylogeny and Bioactivity of a Diverse Collection of Burkholderia
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.09.033878; this version posted April 11, 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 Kill and cure: genomic phylogeny and bioactivity of a diverse collection of Burkholderia 2 gladioli bacteria capable of pathogenic and beneficial lifestyles 3 4 Authors: 5 Cerith Jones1,5, Gordon Webster1, Alex J. Mullins1, Matthew Jenner2,9, Matthew J. Bull1,6, 6 Yousef Dashti2,7, Theodore Spilker3, Julian Parkhill4,8, Thomas R. Connor1, John J. LiPuma3, 7 Gregory L. Challis2,9,10 and Eshwar Mahenthiralingam1# 8 9 Affiliations: 10 1 Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School 11 of Biosciences, Cardiff University, Cardiff, Wales, CF10 3AX, UK 12 13 2 Department of Chemistry, University of Warwick, CV4 7AL, UK 14 15 3 Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA. 16 17 4 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, 18 CB10 1SA UK. 19 20 5 Current address: School of Applied Sciences, Faculty of Computing, Engineering and 21 Science, University of South Wales, Pontypridd, CF37 4BD, UK 22 23 6 Current address: Pathogen Genomics Unit, Public Health Wales Microbiology Cardiff, 24 University Hospital of Wales, Cardiff, CF14 4XW 25 26 7 Current address: The Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, 27 Newcastle University, Newcastle upon Tyne, NE2 4AX, UK 28 29 8 Current address: Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES 30 31 9 Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK 32 33 10 Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, 34 Monash University, Clayton, VIC 3800, Australia 35 36 37 #Corresponding Author: Prof.