CDISC Controlled Terminology SDTM - 2011-06-10
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Biofilm Formation by Moraxella Catarrhalis
BIOFILM FORMATION BY MORAXELLA CATARRHALIS APPROVED BY SUPERVISORY COMMITTEE Eric J. Hansen, Ph.D. ___________________________ Kevin S. McIver, Ph.D. ___________________________ Michael V. Norgard, Ph.D. ___________________________ Philip J. Thomas, Ph.D. ___________________________ Nicolai S.C. van Oers, Ph.D. ___________________________ BIOFILM FORMATION BY MORAXELLA CATARRHALIS by MELANIE MICHELLE PEARSON DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas March, 2004 Copyright by Melanie Michelle Pearson 2004 All Rights Reserved Acknowledgements As with any grand endeavor, there was a large supporting cast who guided me through the completion of my Ph.D. First and foremost, I would like to thank my mentor, Dr. Eric Hansen, for granting me the independence to pursue my ideas while helping me shape my work into a coherent story. I have seen that the time involved in supervising a graduate student is tremendous, and I am grateful for his advice and support. The members of my graduate committee (Drs. Michael Norgard, Kevin McIver, Phil Thomas, and Nicolai van Oers) have likewise given me a considerable investment of time and intellect. Many of the faculty, postdocs, students and staff of the Microbiology department have added to my education and made my experience here positive. Many members of the Hansen laboratory contributed to my work. Dr. Eric Lafontaine gave me my first introduction to M. catarrhalis. I hope I have learned from his example of patience, good nature, and hard work. -
Blocking Transmission of Vector-Borne Diseases
International Journal for Parasitology: Drugs and Drug Resistance 7 (2017) 90e109 Contents lists available at ScienceDirect International Journal for Parasitology: Drugs and Drug Resistance journal homepage: www.elsevier.com/locate/ijpddr Review Blocking transmission of vector-borne diseases * Sandra Schorderet-Weber a, Sandra Noack b, Paul M. Selzer b, Ronald Kaminsky c, a Sablons 30, 2000 Neuchatel,^ Switzerland b Boehringer Ingelheim Animal Health GmbH, Binger Str. 173, 55216 Ingelheim, Germany c ParaC Consulting for Parasitology and Drug Discovery, Altenstein 13, 79685 Haeg-Ehrsberg, Germany article info abstract Article history: Vector-borne diseases are responsible for significant health problems in humans, as well as in companion Received 14 November 2016 and farm animals. Killing the vectors with ectoparasitic drugs before they have the opportunity to pass Accepted 22 January 2017 on their pathogens could be the ideal way to prevent vector borne diseases. Blocking of transmission Available online 30 January 2017 might work when transmission is delayed during blood meal, as often happens in ticks. The recently described systemic isoxazolines have been shown to successfully prevent disease transmission under Keywords: conditions of delayed pathogen transfer. However, if the pathogen is transmitted immediately at bite as it Vector-borne diseases is the case with most insects, blocking transmission becomes only possible if ectoparasiticides prevent Transmission blocking Drug discovery the vector from landing on or, at least, from biting the host. Chemical entities exhibiting repellent activity Speed of kill in addition to fast killing, like pyrethroids, could prevent pathogen transmission even in cases of im- mediate transfer. Successful blocking depends on effective action in the context of the extremely diverse life-cycles of vectors and vector-borne pathogens of medical and veterinary importance which are summarized in this review. -
Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
Review Article Yersinia Enterocolitica: Mode of Transmission, Molecular Insights of Virulence, and Pathogenesis of Infection
SAGE-Hindawi Access to Research Journal of Pathogens Volume 2011, Article ID 429069, 10 pages doi:10.4061/2011/429069 Review Article Yersinia enterocolitica: Mode of Transmission, Molecular Insights of Virulence, and Pathogenesis of Infection Yeasmin Sabina,1 Atiqur Rahman,2 Ramesh Chandra Ray,3 and Didier Montet4 1 Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh 2 Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh 3 Central Tuber Crops Research Institute, Bhubaneswar, India 4 Centre International de Recherche en Agronomie pour le Developpement (CIRAD), Montpellier, France Correspondence should be addressed to Yeasmin Sabina, y [email protected] Received 19 April 2011; Revised 28 May 2011; Accepted 5 June 2011 Academic Editor: Latiful Bari Copyright © 2011 Yeasmin Sabina 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. Although Yersinia enterocolitica is usually transmitted through contaminated food and untreated water, occasional transmission such as human-to-human, animal-to-human and blood transfusion associated transmission have also identified in human disease. Of the six Y. enterocolitica biotypes, the virulence of the pathogenic biotypes, namely, 1B and 2–5 is attributed to the presence of a highly conserved 70-kb virulence plasmid, termed pYV/pCD and certain chromosomal genes. Some biotype 1A strains, despite lacking virulence plasmid (pYV) and traditional chromosomal virulence genes, are isolated frequently from humans with gastrointestinal diseases similar to that produced by isolates belonging known pathogenic biotypes. Y. enterocolitica pathogenic biotypes have evolved two major properties: the ability to penetrate the intestinal wall, which is thought to be controlled by plasmid genes, and the production of heat-stable enterotoxin, which is controlled by chromosomal genes. -
Escherichia Coli Saccharomyces Cerevisiae Bacillus Subtilis はB
研究開発等に係る遺伝子組換え生物等の第二種使用等に当たって執るべき拡散防止措 置等を定める省令の規定に基づき認定宿主ベクター系等を定める件 (平成十六年一月二十九日文部科学省告示第七号) 最終改正:令和三年二月十五日文部科学省告示第十三号 (認定宿主ベクター系) 第一条 研究開発等に係る遺伝子組換え生物等の第二種使用等に当たって執るべき拡散防止 措置等を定める省令(以下「省令」という。)第二条第十三号の文部科学大臣が定める認 定宿主ベクター系は、別表第一に掲げるとおりとする。 (実験分類の区分ごとの微生物等) 第二条 省令第三条の表第一号から第四号までの文部科学大臣が定める微生物等は、別表第 二の上欄に掲げる区分について、それぞれ同表の下欄に掲げるとおりとする。 (特定認定宿主ベクター系) 第三条 省令第五条第一号ロの文部科学大臣が定める特定認定宿主ベクター系は、別表第一 の2の項に掲げる認定宿主ベクター系とする。 (自立的な増殖力及び感染力を保持したウイルス及びウイロイド) 第四条 省令別表第一第一号ヘの文部科学大臣が定めるウイルス及びウイロイドは、別表第 三に掲げるとおりとする。 別表第1(第1条関係) 区 分 名 称 宿主及びベクターの組合せ 1 B1 (1) EK1 Escherichia coli K12株、B株、C株及びW株又は これら各株の誘導体を宿主とし、プラスミド又は バクテリオファージの核酸であって、接合等によ り宿主以外の細菌に伝達されないものをベクター とするもの(次項(1)のEK2に該当するものを除 く。) (2) SC1 Saccharomyces cerevisiae又はこれと交雑可能な 分類学上の種に属する酵母を宿主とし、これらの 宿主のプラスミド、ミニクロモソーム又はこれら の誘導体をベクターとするもの(次項(2)のSC2 に該当するものを除く。) (3) BS1 Bacillus subtilis Marburg168株、この誘導体又 はB. licheniformis全株のうち、アミノ酸若しく は核酸塩基に対する複数の栄養要求性突然変異を 有する株又は胞子を形成しない株を宿主とし、こ れらの宿主のプラスミド(接合による伝達性のな いものに限る。)又はバクテリオファージの核酸 をベクターとするもの(次項(3)のBS2に該当す るものを除く。) (4) Thermus属細菌 Thermus属細菌(T. thermophilus、T. aquaticus、 T. flavus、T. caldophilus及びT. ruberに限る。) を宿主とし、これらの宿主のプラスミド又はこの 誘導体をベクターとするもの (5) Rhizobium属細菌 Rhizobium属細菌(R. radiobacter(別名Agroba- cterium tumefaciens)及びR. rhizogenes(別名 Agrobacterium rhizogenes)に限る。)を宿主と し、これらの宿主のプラスミド又はRK2系のプラ スミドをベクターとするもの (6) Pseudomonas putida Pseudomonas putida KT2440株又はこの誘導体を 宿主とし、これら宿主への依存性が高く、宿主以 外の細胞に伝達されないものをベクターとするも の (7) Streptomyces属細菌 Streptomyces属細菌(S. avermitilis、S. coel- icolor [S. violaceoruberとして分類されるS. coelicolor A3(2)株を含む]、S. lividans、S. p- arvulus、S. griseus及びS. -
Downloads/Bin/Fastq Quality Filter -Q20 -P90 -Q33
Biological Reduction of Selenium Oxyanions in the Presence of Nitrate anions using Anaerobic Microbes by Gaurav Subedi B.Sc., Jacobs University Bremen, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2016 © Gaurav Subedi, 2016 Abstract Biological selenium reduction has emerged as a viable solution for the removal of toxic selenium from the environment. However, the presence of nitrate hinders selenium reduction by acting as a competitive electron acceptor. The present thesis investigated the use of local mine-impacted sediment as an inoculum for selenium reduction and studied the affect of nitrate on the removal of selenium. Sediment samples, impacted by mining activities, were collected from two vastly different sites of the Elk River Valley. These sediments namely; Goddard Marsh and Mature Tailing Coal, were enriched for selenium reducing bacterial consortium under high selenium and varying nitrate concentrations to put additional selection pressure. Ultimately, two cultures from Goddard Marsh enriched under low and high nitrate condition as well as one culture from Mature Tailing Coal enriched under moderate nitrate condition were used to access the affect of nitrate on selenium reduction using central composite design matrix. The extent of Se reduction was highest in the Goddard Marsh enrichment with no nitrate while enrichment with moderate and high nitrate reduced selenium poorly. ANOVA results from the CCD experiment in Goddard Marsh enrichment with no nitrate indicated no affect of nitrate in Se reduction. Two primer sets targeting the selenate redutase (serA) from Thauera selenatis and nitrite reductase (nirK) from denitrifying population were used to quantify the population of selenium reducing and denitrifying population in the CCD experiment. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk- standards-for-microbiology-investigations-smi-quality-and-consistency-in-clinical- laboratories. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for-microbiology-investigations- steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
Pdfs/ Ommended That Initial Cultures Focus on Common Pathogens, Pscmanual/9Pscssicurrent.Pdf)
Clinical Infectious Diseases IDSA GUIDELINE A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya J. Michael Miller,1 Matthew J. Binnicker,2 Sheldon Campbell,3 Karen C. Carroll,4 Kimberle C. Chapin,5 Peter H. Gilligan,6 Mark D. Gonzalez,7 Robert C. Jerris,7 Sue C. Kehl,8 Robin Patel,2 Bobbi S. Pritt,2 Sandra S. Richter,9 Barbara Robinson-Dunn,10 Joseph D. Schwartzman,11 James W. Snyder,12 Sam Telford III,13 Elitza S. Theel,2 Richard B. Thomson Jr,14 Melvin P. Weinstein,15 and Joseph D. Yao2 1Microbiology Technical Services, LLC, Dunwoody, Georgia; 2Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota; 3Yale University School of Medicine, New Haven, Connecticut; 4Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland; 5Department of Pathology, Rhode Island Hospital, Providence; 6Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill; 7Department of Pathology, Children’s Healthcare of Atlanta, Georgia; 8Medical College of Wisconsin, Milwaukee; 9Department of Laboratory Medicine, Cleveland Clinic, Ohio; 10Department of Pathology and Laboratory Medicine, Beaumont Health, Royal Oak, Michigan; 11Dartmouth- Hitchcock Medical Center, Lebanon, New Hampshire; 12Department of Pathology and Laboratory Medicine, University of Louisville, Kentucky; 13Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts; 14Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, Illinois; and 15Departments of Medicine and Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey Contents Introduction and Executive Summary I. -
Antibiotic Use Guidelines for Companion Animal Practice (2Nd Edition) Iii
ii Antibiotic Use Guidelines for Companion Animal Practice (2nd edition) iii Antibiotic Use Guidelines for Companion Animal Practice, 2nd edition Publisher: Companion Animal Group, Danish Veterinary Association, Peter Bangs Vej 30, 2000 Frederiksberg Authors of the guidelines: Lisbeth Rem Jessen (University of Copenhagen) Peter Damborg (University of Copenhagen) Anette Spohr (Evidensia Faxe Animal Hospital) Sandra Goericke-Pesch (University of Veterinary Medicine, Hannover) Rebecca Langhorn (University of Copenhagen) Geoffrey Houser (University of Copenhagen) Jakob Willesen (University of Copenhagen) Mette Schjærff (University of Copenhagen) Thomas Eriksen (University of Copenhagen) Tina Møller Sørensen (University of Copenhagen) Vibeke Frøkjær Jensen (DTU-VET) Flemming Obling (Greve) Luca Guardabassi (University of Copenhagen) Reproduction of extracts from these guidelines is only permitted in accordance with the agreement between the Ministry of Education and Copy-Dan. Danish copyright law restricts all other use without written permission of the publisher. Exception is granted for short excerpts for review purposes. iv Foreword The first edition of the Antibiotic Use Guidelines for Companion Animal Practice was published in autumn of 2012. The aim of the guidelines was to prevent increased antibiotic resistance. A questionnaire circulated to Danish veterinarians in 2015 (Jessen et al., DVT 10, 2016) indicated that the guidelines were well received, and particularly that active users had followed the recommendations. Despite a positive reception and the results of this survey, the actual quantity of antibiotics used is probably a better indicator of the effect of the first guidelines. Chapter two of these updated guidelines therefore details the pattern of developments in antibiotic use, as reported in DANMAP 2016 (www.danmap.org). -
Download/Issues/Mining/Reference Guide to Treatment Technologi Es for MIW.Pdf
Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water by Frank Nkansah - Boadu BSc., Kwame Nkrumah University of Science and Technology, 2003 MASc., The University of British Columbia, 2013 A DISSERTATION SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Chemical and Biological Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) December 2019 © Frank Nkansah - Boadu, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, the dissertation entitled: Removal of Soluble Selenium in the Presence of Nitrate from Coal Mining-Influenced Water submitted by Frank Nkansah-Boadu in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Chemical and Biological Engineering Examining Committee: Susan Baldwin, Chemical and Biological Engineering Supervisor Vikramaditya Yadav, Chemical and Biological Engineering Supervisory Committee Member Troy Vassos, Adjunct Professor, Civil Engineering Supervisory Committee Member Anthony Lau, Chemical and Biological Engineering University Examiner Scott Dunbar, Mining Engineering University Examiner ii Abstract Biological treatment to remove dissolved selenium from mining-influenced water (MIW) is inhibited by co-contaminants, especially nitrate. It was hypothesized that selenium reducing microorganisms can be obtained from native mine bacteria at sites affected by MIW due to the selection pressure from elevated selenium concentrations at those sites. Enrichment of these microorganisms and testing of their capacity to remove dissolved selenium from actual coal MIW was the objective of this dissertation. Fifteen sediments were collected from eleven different vegetated or non-vegetated seepage collection ponds and one non-impacted natural wetland. -
Phase and Antigenic Variation Mediated by Genome Modifications
Antonie van Leeuwenhoek (2008) 94:493–515 DOI 10.1007/s10482-008-9267-6 REVIEW PAPER Phase and antigenic variation mediated by genome modifications Florence Wisniewski-Dye´ Æ Ludovic Vial Received: 6 April 2008 / Accepted: 9 July 2008 / Published online: 29 July 2008 Ó Springer Science+Business Media B.V. 2008 Abstract Phase and antigenic variation is used by Keywords Adaptation Á Antigenic variation Á several bacterial species to generate intra-population Genome plasticity Á Phenotypic switch diversity that increases bacterial fitness and is important in niche adaptation, or to escape host defences. By this adaptive process, bacteria undergo frequent and usually reversible phenotypic changes Introduction resulting from genetic or epigenetic alterations at specific genetic loci. Phase variation or phenotypic One of the most obvious features of phase variation is switch allows the expression of a given phenotype to the appearance of a minority of colonies or colony be switched ON or OFF. Antigenic variation refers to sectors displaying a different aspect. Phase variation the expression of a number of alternative forms of an or phenotypic switch is used by several bacterial antigen on the cell surface, and at a molecular level, species to generate intra-population diversity that shares common features with phase variation mech- increases bacterial fitness and is important in niche anisms. This review will focus on phase and antigenic adaptation, or to escape host defences. Phase varia- variation mechanisms implying genome modifica- tion allows that the expression of a given phenotype tions, with an emphasis on the diversity of is either ON or OFF; these events are usually phenotypes regulated by these mechanisms, and the reversible (ON $ OFF) but may be irreversible ecological relevance of variant appearance within a (ON ? OFF or OFF ? ON), and result from genetic given population. -
Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella Multocida Isolates from Pneumonic Cases of Cattle in Ethiopia
Phenotypic and Molecular Characterization of the Capsular Serotypes of Pasteurella multocida Isolates from Pneumonic Cases of Cattle in Ethiopia Mirtneh Akalu Yilma ( [email protected] ) Koneru Lakshmaiah Education Foundation https://orcid.org/0000-0001-5936-6873 Murthy Bhadra Vemulapati Koneru Lakshmaiah Education Foundation Takele Abayneh Tefera Veterinaerinstituttet Martha Yami VeterinaryInstitute Teferi Degefa Negi VeterinaryInstitue Alebachew Belay VeterinaryInstitute Getaw Derese VeterinaryInstitute Esayas Gelaye Leykun Veterinaerinstituttet Research article Keywords: Biovar, Capsular type, Cattle, Ethiopia, Pasteurella multocida Posted Date: January 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-61749/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract Background: Pasteurella multocida is a heterogeneous species and opportunistic pathogen associated with pneumonia in cattle. Losses due to pneumonia and associated expenses are estimated to be higher in Ethiopia with limited information about the distribution of capsular serotypes. Hence, this study was designed to determine the phenotypic and capsular serotypes of P. multocida from pneumonic cases of cattle. Methods: A cross sectional study with purposive sampling method was employed in 400 cattle from April 2018 to January 2019. Nasopharyngeal swabs and lung tissue samples were collected from clinically suspected pneumonic cases of calves (n = 170) and adult cattle (n = 230). Samples were analyzed using bacteriological and molecular assay. Results: Bacteriological analysis revealed isolation of 61 (15.25%) P. multocida subspecies multocida. Incidence was higher in calves 35 (57.38%) compared to adult cattle 26 (42.62%) at P < 0.5. PCR assay targeting KMT1 gene (~460 bp) conrmed P.