Afipia Clevelandensis Sp
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Proquest Dissertations
Approaches to assessing microbial communities in soil, two examples: Biosurfactant production and phenanthrene degradation Item Type text; Dissertation-Reproduction (electronic) Authors Bodour, Adria Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 01/10/2021 06:55:39 Link to Item http://hdl.handle.net/10150/280136 INFORMATION TO USERS This manuscript has been reproduced from the microfiinn master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand corner and continuing from left to right in equal -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Bartonella: Feline Diseases and Emerging Zoonosis
BARTONELLA: FELINE DISEASES AND EMERGING ZOONOSIS WILLIAM D. HARDY, JR., V.M.D. Director National Veterinary Laboratory, Inc. P.O Box 239 Franklin Lakes, New Jersey 07417 201-891-2992 www.natvetlab.com or .net Gingivitis Proliferative Gingivitis Conjunctivitis/Blepharitis Uveitis & Conjunctivitis URI Oral Ulcers Stomatitis Lymphadenopathy TABLE OF CONTENTS Page SUMMARY……………………………………………………………………………………... i INTRODUCTION……………………………………………………………………………… 1 MICROBIOLOGY……………………………………………………………………………... 1 METHODS OF DETECTION OF BARTONELLA INFECTION.………………………….. 1 Isolation from Blood…………………………………………………………………….. 2 Serologic Tests…………………………………………………………………………… 2 SEROLOGY……………………………………………………………………………………… 3 CATS: PREVALENCE OF BARTONELLA INFECTIONS…………………………………… 4 Geographic Risk factors for Infection……………………………………………………. 5 Risk Factors for Infection………………………………………………………………… 5 FELINE BARTONELLA DISEASES………………………………………………………….… 6 Bartonella Pathogenesis………………………………………………………………… 7 Therapy of Feline Bartonella Diseases…………………………………………………… 14 Clinical Therapy Results…………………………………………………………………. 15 DOGS: PREVALENCE OF BARTONELLA INFECTIONS…………………………………. 17 CANINE BARTONELLA DISEASES…………………………………………………………... 17 HUMAN BARTONELLA DISEASES…………………………………………………………… 18 Zoonotic Case Study……………………………………………………………………... 21 FELINE BLOOD DONORS……………………………………………………………………. 21 REFERENCES………………………………………………………………………………….. 22 This work was initiated while Dr. Hardy was: Professor of Medicine, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York and Director, -
A Distinct Pathway for Tetrahymanol Synthesis in Bacteria
A distinct pathway for tetrahymanol synthesis in bacteria Amy B. Banta1, Jeremy H. Wei1, and Paula V. Welander2 Department of Earth System Science, Stanford University, Stanford, CA 94305 Edited by John M. Hayes, Woods Hole Oceanographic Institution, Berkeley, CA, and approved September 25, 2015 (received for review June 11, 2015) Tetrahymanol is a polycyclic triterpenoid lipid first discovered in the physiological role of tetrahymanol in bacteria is unknown. Recent ciliate Tetrahymena pyriformis whose potential diagenetic product, studies have highlighted increased tetrahymanol production in gammacerane, is often used as a biomarker for water column strat- R. palustris TIE-1 under certain physiological conditions (e.g., ification in ancient ecosystems. Bacteria are also a potential source photoautotrophic growth) and also when cellular hopanoid lipid of tetrahymanol, but neither the distribution of this lipid in extant profiles are altered in gene deletion mutants (22, 23), but the bacteria nor the significance of bacterial tetrahymanol synthesis for physiological significance of these changes is not known. Further, interpreting gammacerane biosignatures is known. Here we couple the biochemical mechanism of tetrahymanol synthesis in bacteria comparative genomics with genetic and lipid analyses to link a pro- is unclear. In ciliates, squalene-tetrahymanol cyclase (Stc) cata- tein of unknown function to tetrahymanol synthesis in bacteria. This tetrahymanol synthase (Ths) is found in a variety of bacterial lyzes the cyclization of squalene directly to tetrahymanol (24), but genomes, including aerobic methanotrophs, nitrite-oxidizers, and neither of the two known bacterial tetrahymanol producers harbor sulfate-reducers, and in a subset of aquatic and terrestrial metage- a copy of Stc (10, 24). -
Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.29.067207; this version posted April 30, 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. Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes Robert J. Huddy1,2, Rohan Sachdeva3, Fadzai Kadzinga1,2, Rose Kantor4, Susan T.L. Harrison1,2 and Jillian F. Banfield3,4,5,6* 1The Center for Bioprocess Engineering Research, University of Cape Town, South Africa 2The Future Water Institute, University of Cape Town, South Africa 3The Innovative Genomics Institute at the University of California, Berkeley, California, USA 4The Department of Earth and Planetary Science, University of California, Berkeley, California, USA 5The Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA 6The University of Melbourne, Victoria, Australia *Corresponding Author: [email protected] Abstract Thiocyanate (SCN-) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCN- degrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCN- degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN- could be reproducibly selected for based on SCN- loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN- contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN- degrading consortium. -
Genetic and Phenetic Analyses of Bradyrhizobium Strains Nodulating Peanut (Arachis Hypogaea L.) Roots DIMAN VAN ROSSUM,1 FRANK P
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Apr. 1995, p. 1599–1609 Vol. 61, No. 4 0099-2240/95/$04.0010 Copyright q 1995, American Society for Microbiology Genetic and Phenetic Analyses of Bradyrhizobium Strains Nodulating Peanut (Arachis hypogaea L.) Roots DIMAN VAN ROSSUM,1 FRANK P. SCHUURMANS,1 MONIQUE GILLIS,2 ARTHUR MUYOTCHA,3 1 1 1 HENK W. VAN VERSEVELD, ADRIAAN H. STOUTHAMER, AND FRED C. BOOGERD * Department of Microbiology, Institute for Molecular Biological Sciences, Vrije Universiteit, BioCentrum Amsterdam, 1081 HV Amsterdam, The Netherlands1; Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Ghent, Belgium2; and Soil Productivity Research Laboratory, Marondera, Zimbabwe3 Received 15 August 1994/Accepted 10 January 1995 Seventeen Bradyrhizobium sp. strains and one Azorhizobium strain were compared on the basis of five genetic and phenetic features: (i) partial sequence analyses of the 16S rRNA gene (rDNA), (ii) randomly amplified DNA polymorphisms (RAPD) using three oligonucleotide primers, (iii) total cellular protein profiles, (iv) utilization of 21 aliphatic and 22 aromatic substrates, and (v) intrinsic resistances to seven antibiotics. Partial 16S rDNA analysis revealed the presence of only two rDNA homology (i.e., identity) groups among the 17 Bradyrhizobium strains. The partial 16S rDNA sequences of Bradyrhizobium sp. strains form a tight similarity (>95%) cluster with Rhodopseudomonas palustris, Nitrobacter species, Afipia species, and Blastobacter denitrifi- cans but were less similar to other members of the a-Proteobacteria, including other members of the Rhizobi- aceae family. Clustering the Bradyrhizobium sp. strains for their RAPD profiles, protein profiles, and substrate utilization data revealed more diversity than rDNA analysis. Intrinsic antibiotic resistance yielded strain- specific patterns that could not be clustered. -
Genome Sequencing and Annotation of Afipia Septicemium Strain OHSU II
ÔØ ÅÒÙ×Ö ÔØ Genome sequencing and annotation of Afipia septicemium strain OHSU II Philip Yang, Guo-Chiuan Hung, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai, Shyh-Ching Lo PII: S2213-5960(14)00033-6 DOI: doi: 10.1016/j.gdata.2014.06.001 Reference: GDATA 43 To appear in: Genomics Data Received date: 13 May 2014 Revised date: 2 June 2014 Accepted date: 2 June 2014 Please cite this article as: Philip Yang, Guo-Chiuan Hung, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai, Shyh-Ching Lo, Genome sequencing and annotation of Afipia septicemium strain OHSU II, Genomics Data (2014), doi: 10.1016/j.gdata.2014.06.001 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. ACCEPTED MANUSCRIPT Data in Brief Title: Genome sequencing and annotation of Afipia septicemium strain OHSU_II Authors: Philip Yang1, Guo-Chiuan Hung1, Haiyan Lei, Tianwei Li, Bingjie Li, Shien Tsai and Shyh-Ching Lo* 1 Both are first authors, equally contributed * Corresponding author Tel/Fax +1-301-827-3170/+1-301-827-0449 Email address: [email protected] Affiliations: Tissue Microbiology Laboratory, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA Abstract We report the 5.1 Mb noncontiguous draft genome of Afipia septicemium strain OHSU_II, isolated from blood of a female patient. -
Microbial Dynamics in the Aquatic Environments of a Nuclear Reactor
Ph.D. thesis in Bioscience engineering Valérie Van Eesbeeck Microbial dynamics in the aquatic environments of a nuclear reactor PhD dissertation committee Supervisors: Dr. Natalie Leys (SCK CEN – Microbiology Unit) Prof. Jacques Mahillon (UCL – Earth and Life Institute) Reviewers: Prof. Claude Bragard (UCL – Earth and Life Institute) Dr. Pieter Monsieurs (ITG – protozoan pathogen units) Dr. Corinne Rivasseau (CEA – laboratory of plant cellular physiology) Prof. Jonathan Lloyd (Earth and Environmental Sciences – University of Manchester) President: Prof. Emmanuel Hanert (UCL – Earth and Life Institute) Acknowledgments This PhD has been an incredible journey, throughout which I was fortunate enough to be supported by a wonderful group of people. I can truly say that without them, this endeavor would not have been successful. First of all, I would like to express my deepest gratitude to my SCK CEN mentors Natalie Leys and Pieter Monsieurs, whose support and advice have been unwavering throughout this entire PhD. Thank you for your valuable scientific insights and suggestions, and most of all thank you for encouraging me when times were hard and never giving up on me! Thank you for allowing me the space I needed to bring this project to fruition. I would also like to immensely thank my UCL supervisor Prof. Jacques Mahillon, whose warm guidance and support kept me on track during difficult times. Thank you for the interesting discussions and for always keeping an open door for me. I will always cherish your light-hearted and humorous touch. Next, I would like to thank Prof. Claude Bragard, Dr. Corinne Rivasseau, Prof. Jonathan Lloyd and Prof. -
Periodontite Crônica Generalizada (PCG) E Periodontite Agressiva Generalizada (PAG) Para Avaliar Diferenças Entre Suas Microbiotas
SÉRGIO EDUARDO BRAGA DA CRUZ ANÁLISE BIOMOLECULAR DE COMUNIDADES MICROBIANAS SUBGENGIVAIS ASSOCIADAS ÀS PERIODONTITES CRÔNICA E AGRESSIVA GENERALIZADAS Tese apresentada à Faculdade de Odontologia de Piracicaba, da Universidade Estadual de Campinas, para obtenção do Título de Doutor em Biologia Buco-Dental, área de Microbiologia Oral e Imunologia. Orientador: Prof. Dr. Reginaldo Bruno Gonçalves Co-orientador: Prof. Dr. Daniel Saito PIRACICABA, 2010 I II Dedico este trabalho aos meus pais Marilene e João Batista que sempre me apoiaram em todos meus momentos e decisões e por todo amor que sempre me deram. Vocês serão sempre exemplos de vida, dignidade, luta e honra! Às minhas irmãs Monalisa e Renata Karina pela amizade, carinho e amor. Muito obrigado! Eu vos amo! III AGRADECIMENTOS Agradeço a Deus, por cada dia a mim oferecido e pelas oportunidades que tenho a cada dia para crescer e aprender. Ao Prof. Dr. Reginaldo Bruno Gonçalves, meus sinceros e eternos agradecimentos pela orientação, pelo exemplo de batalha profissional, e por todo apoio aqui no Brasil e no Canadá. Ao Prof. Dr. Daniel Saito por todo apoio, co-orientação, ensinamentos e ajuda durante o meu doutorado. Ao Prof. Dr. José Franciso Höfling pelos ensinamentos e conhecimentos laboratoriais e por todo apoio oferecido. À Profª. Drª. Renata de Oliveira Mattos-Graner pelos conhecimentos repassados, pela orientação durante o meu programa de estágio docente (PED) e por todo apoio. Ao Rafael Nóbrega Stipp pela amizade, companheirismo, exemplo profissional, por todos os ensinamentos na área de biologia molecular e microbiologia e, obviamente, pelos grandes momentos de churrascos que em muito fizeram minha história aqui em Piracicaba. -
Recombinase in Trio (RIT) Elements in Bacterial Genomes: Assessing the Distribution and Mobility of a Novel Yet Widespread Set of Mobile Genes
Recombinase in Trio (RIT) Elements in Bacterial Genomes: Assessing the Distribution and Mobility of a Novel yet Widespread Set of Mobile Genes. by Nicole Dorothy Ricker A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Physical and Environmental Sciences University of Toronto Scarborough © Copyright by Nicole Ricker 2016 Recombinase in Trio (RIT) Elements in Bacterial Genomes: Assessing the Distribution and Mobility of a Novel yet Widespread Set of Mobile Genes. Nicole Dorothy Ricker Doctor of Philosophy Department of Physical and Environmental Sciences University of Toronto Scarborough 2016 Abstract The research performed over the course of my doctorate training outlines the environmental distribution, mobility, expression and potential role of a newly described family of mobile elements as well as providing valuable information on the challenges and potential benefits of environmental metagenomics. Sequencing technologies have evolved considerably over the course of this work, and evaluating the limitations and opportunities provided by these evolving technologies has formed a significant portion of my thesis work. The remainder of the work has been dedicated to understanding the distribution and mechanisms of Recombinase in Trio (RIT) elements, a previously underappreciated mobile element found in a large diversity of strains, but predominantly in non- pathogenic bacteria. Recombinase in Trio (RIT) elements contain three tyrosine-based site-specific recombinases and display a characteristic gene order and repeat architecture that is conserved across 7 bacterial phyla (Van Houdt et al. 2006; Van Houdt et al. 2012; Ricker et al. 2013). RIT elements have been postulated to be mobile due to the occurrence of multiple identical copies within individual genomes, and are commonly found on plasmids and in genomic islands, including plant symbiosis and catabolic islands. -
Genome-Informed Bradyrhizobium Taxonomy: Where to from Here?
Systematic and Applied Microbiology 42 (2019) 427–439 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Genome-informed Bradyrhizobium taxonomy: where to from here? a a a a,b Juanita R. Avontuur , Marike Palmer , Chrizelle W. Beukes , Wai Y. Chan , a c d e Martin P.A. Coetzee , Jochen Blom , Tomasz Stepkowski˛ , Nikos C. Kyrpides , e e f a Tanja Woyke , Nicole Shapiro , William B. Whitman , Stephanus N. Venter , a,∗ Emma T. Steenkamp a Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa b Biotechnology Platform, Agricultural Research Council Onderstepoort Veterinary Institute (ARC-OVI), Onderstepoort 0110, South Africa c Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany d Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Poland e DOE Joint Genome Institute, Walnut Creek, CA, United States f Department of Microbiology, University of Georgia, Athens, GA, United States a r t i c l e i n f o a b s t r a c t Article history: Bradyrhizobium is thought to be the largest and most diverse rhizobial genus, but this is not reflected in Received 1 February 2019 the number of described species. Although it was one of the first rhizobial genera recognised, its taxon- Received in revised form 26 March 2019 omy remains complex. Various contemporary studies are showing that genome sequence information Accepted 26 March 2019 may simplify taxonomic decisions. Therefore, the growing availability of genomes for Bradyrhizobium will likely aid in the delineation and characterization of new species. -
Development of a System for Genetic Manipulation of Bartonella Bacilliformis
University of Montana ScholarWorks at University of Montana Graduate Student Theses, Dissertations, & Professional Papers Graduate School 1998 Development of a system for genetic manipulation of Bartonella bacilliformis James M. Battisti The University of Montana Follow this and additional works at: https://scholarworks.umt.edu/etd Let us know how access to this document benefits ou.y Recommended Citation Battisti, James M., "Development of a system for genetic manipulation of Bartonella bacilliformis" (1998). Graduate Student Theses, Dissertations, & Professional Papers. 10534. https://scholarworks.umt.edu/etd/10534 This Dissertation is brought to you for free and open access by the Graduate School at ScholarWorks at University of Montana. It has been accepted for inclusion in Graduate Student Theses, Dissertations, & Professional Papers by an authorized administrator of ScholarWorks at University of Montana. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely afreet reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps.