Understanding the Ecology and Epidemiology of Pythium Violae to Enable Disease Management in Carrot Crops Kathryn R
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Phytopythium: Molecular Phylogeny and Systematics
Persoonia 34, 2015: 25–39 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158515X685382 Phytopythium: molecular phylogeny and systematics A.W.A.M. de Cock1, A.M. Lodhi2, T.L. Rintoul 3, K. Bala 3, G.P. Robideau3, Z. Gloria Abad4, M.D. Coffey 5, S. Shahzad 6, C.A. Lévesque 3 Key words Abstract The genus Phytopythium (Peronosporales) has been described, but a complete circumscription has not yet been presented. In the present paper we provide molecular-based evidence that members of Pythium COI clade K as described by Lévesque & de Cock (2004) belong to Phytopythium. Maximum likelihood and Bayesian LSU phylogenetic analysis of the nuclear ribosomal DNA (LSU and SSU) and mitochondrial DNA cytochrome oxidase Oomycetes subunit 1 (COI) as well as statistical analyses of pairwise distances strongly support the status of Phytopythium as Oomycota a separate phylogenetic entity. Phytopythium is morphologically intermediate between the genera Phytophthora Peronosporales and Pythium. It is unique in having papillate, internally proliferating sporangia and cylindrical or lobate antheridia. Phytopythium The formal transfer of clade K species to Phytopythium and a comparison with morphologically similar species of Pythiales the genera Pythium and Phytophthora is presented. A new species is described, Phytopythium mirpurense. SSU Article info Received: 28 January 2014; Accepted: 27 September 2014; Published: 30 October 2014. INTRODUCTION establish which species belong to clade K and to make new taxonomic combinations for these species. To achieve this The genus Pythium as defined by Pringsheim in 1858 was goal, phylogenies based on nuclear LSU rRNA (28S), SSU divided by Lévesque & de Cock (2004) into 11 clades based rRNA (18S) and mitochondrial DNA cytochrome oxidase1 (COI) on molecular systematic analyses. -
Apch 2017 Delegates' Abstract
APCH 2017 DELEGATES’ ABSTRACT Topic: Basic Science: Genetics, genomics, proteomics and metabolomics Abstract No: 3630 A PILOT GENOME WIDE ASSOCIATION STUDY (GWAS) IN MULTI ETHNIC POPULATION OF MALAYSIA Ms Syahirah Kaja Mohideen*1 ; Prof Datuk Dr A Rahman A Jamal1 ; Prof Dr Nor Azmi Kamaruddin1 ; Prof Dr Norlela Sukor1 ; Ms Elena Aisha Azizan1 1MEDICINE/ UNIVERSITI KEBANGSAAN MALAYSIA (UKM)/ Malaysia Objective Primary aldosteronism (PA) occurs due to the presence of aldosterone-producing lesions commonly located in the adrenal gland which can thus be cured by an adrenalectomy. Studies on surgically removed tissues found somatic mutations in five genes (KCNJ5, ATP1A1, ATP2B3, CACNA1D, and CTNNB1) can cause the excess aldosterone production. Most of these studies were performed in Caucasian patients. The aim of our study is to understand the genetic background which may promote somatic mutation in these genes and to investigate the frequency and distribution of these somatic mutations in the multiethnic Asian population in Malaysia. Method To characterize the genetic background of PA, a pilot genome wide association study (GWAS) was performed using the Human Infinium OmniExpressExome-8 v1.4 BeadChip containing 960,919 markers to compare gDNA of PA patients with healthy controls. The Association Workflow in Partek® Genomics SuiteTM was used for quality control and association analysis was performed using the Chi-square Test and reported as an odds ratio (OR). On tumour DNA, targeted sequencing of hotspots for the five causal genes were performed. Discussion From the pilot GWAS, two SNPs in chromosome 2 were identified to be associated with PA (OR=11.03, P-value=7.1x10-10, and OR=1.61, P-value=4.0x10-9,). -
U.S. EPA, Pesticides, Label, V-10161 4 SC, 4/20/2011
--- -..:.--~--- ~- ~- >- --=---==-- -"--====- c· ott! 2£lll C '" . zo( UNITED STATES ENVI~ONMENTAL PROTECTION AGENCY WASHINGTON, DC 20460 OFFICE OF CHEMICAL SAFElY AND POLLUTION PREVENTION APR 2 0 20H Robert Hamilton Valent USA Corporation Registration & Regulatory Affairs 1101 14th Street, N.W., Suite 1050 Washington, DC 20005 SUBJECT: Label Amendment V-101614SC EPA Reg. No. 59639-140; Decisions 409896; 420444; 9F7617 (D420455) Submissions Dated April 30, 2009; September 16, 2009 Dear Mr. Hamilton: The revised master and supplemental labels (your version 3/15/2011) referred to above, submi~ed in connection with registration under the Federal Insecticide Fungicide and Rodenticide Act (FIFRA), as amended, to add carrot, potato, and sugarbeet which, with existing crops allows listing of the entire "Root and Tuber Vegetables-Crop Group 1"; and which adds "Brassica, Leafy Greens Subgroup 5B" which, with existing crops allows listing the entire "Bras sica (Cole) Leafy Vegetables, Crop Group 5", all of this in detail as per final rule published 4/20/2011, are acceptable provided the following label changes and conditional data are satisfied ' by specified due dates: 1. At the top of page 1 delete the right and left parentheses from "(Fungicide)" because the rest of this label does the same and we understand the primary brand name to be the "V-10161 4SC Fungicide"; also add a comma after "(Except Brassica Vegetables)," and on page 2 in the First Aid section in the subheading "If on skin or Clothing", make the "C" in "Clothing" lower case and add a period at the end of the last bullet. 2. On page 3 in the Agricultural Use Requirements box, first line; add "(WPS)" after "Worker Protection Standard". -
Pythium Species Associated with Rooibos, and the Influence of Management Practices on Disease Development
PYTHIUM SPECIES ASSOCIATED WITH ROOIBOS, AND THE INFLUENCE OF MANAGEMENT PRACTICES ON DISEASE DEVELOPMENT By AMIRHOSSEIN BAHRAMISHARIF Thesis presented in partial fulfilment of the requirements for the degree of Master of Science in the Faculty of AgriSciences at the University of Stellenbosch Supervisor: Dr. Adéle McLeod Co-supervisor: Dr. Sandra C. Lamprecht March 2012 Stellenbosch University http://scholar.sun.ac.za DECLARATION By submitting this thesis electronically, I declare that the entirety of the work contained therein is my own, original work, that I am the owner of the copyright thereof (unless to the extent explicitly otherwise stated) and that I have not previously in its entirety or in part submitted it for obtaining any qualification. Amirhossein Bahramisharif Date:……………………….. Copyright © 2012 Stellenbosch University All rights reserved Stellenbosch University http://scholar.sun.ac.za PYTHIUM SPECIES ASSOCIATED WITH ROOIBOS, AND THE INFLUENCE OF MANAGEMENT PRACTICES ON DISEASE DEVELOPMENT SUMMARY Damping-off of rooibos (Aspalathus linearis), which is an important indigenous crop in South Africa, causes serious losses in rooibos nurseries and is caused by a complex of pathogens of which oomycetes, mainly Pythium, are an important component. The management of damping-off in organic rooibos nurseries is problematic, since phenylamide fungicides may not be used. Therefore, alternative management strategies such as rotation crops, compost and biological control agents, must be investigated. The management of damping-off requires knowledge, which currently is lacking, of the Pythium species involved, and their pathogenicity towards rooibos and two nursery rotation crops (lupin and oats). Pythium species identification can be difficult since the genus is complex and consists of more than 120 species. -
In Silico Structure-Function, Specificity and Stability Studies of N-Terminal Nucleophile Hydrolase Enzymes
IN SILICO STRUCTURE-FUNCTION, SPECIFICITY AND STABILITY STUDIES OF N-TERMINAL NUCLEOPHILE HYDROLASE ENZYMES THESIS SUBMITTED TO SAVITRIBAI PHULE PUNE UNIVERSITY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN BIOTECHNOLOGY BY PRIYABRATA PANIGRAHI RESEARCH GUIDE Dr. C.G. SURESH DIVISION OF BIOCHEMICAL SCIENCES CSIR-NATIONAL CHEMICAL LABORATORY DR HOMI BHABHA ROAD, PUNE 411008 MAHARASHTRA, INDIA JUNE 2015 DECLARATION BY THE CANDIDATE I hereby declare that the thesis entitled “In silico structure-function, specificity and stability studies of N-terminal nucleophile hydrolase enzymes” submitted by me for the degree of Doctor of Philosophy is the record of work carried out by me during the period from July 2011 to June 2015 under the guidance of Dr. C.G. Suresh, Chief Scientist and has not formed the basis for the award of any degree, diploma, associateship, fellowship, titles in this or any other University or other institution of higher learning. I further declare that the material obtained from other sources has been duly acknowledged in the thesis. Priyabrata Panigrahi Division of Biochemical Sciences CSIR-National Chemical Laboratory Pune - 411 008 June 2015 Acknowledgement This thesis is the end of my journey towards obtaining Ph.D. It would not have been possible to accomplish this without the help, support and encouragement from many people including my well wishers, my friends and colleagues. I would like to express my thanks to everyone who have made this thesis possible and gave me an unforgettable experience. First and foremost, I would like to thank beloved BapDada and Brahmakumaris World Spiritual University for giving me inner strength and willpower to pursue this journey and also their staunch support during tough times. -
The Pennsylvania State University
The Pennsylvania State University The Graduate School Department of Plant Pathology and Environmental Microbiology CHARACTERIZATION OF Pythium and Phytopythium SPECIES FREQUENTLY FOUND IN IRRIGATION WATER A Thesis in Plant Pathology by Carla E. Lanze © 2015 Carla E. Lanze Submitted in Partial Fulfillment of the Requirement for the Degree of Master of Science August 2015 ii The thesis of Carla E. Lanze was reviewed and approved* by the following Gary W. Moorman Professor of Plant Pathology Thesis Advisor David M. Geiser Professor of Plant Pathology Interim Head of the Department of Plant Pathology and Environmental Microbiology Beth K. Gugino Associate Professor of Plant Pathology Todd C. LaJeunesse Associate Professor of Biology *Signatures are on file in the Graduate School iii ABSTRACT Some Pythium and Phytopythium species are problematic greenhouse crop pathogens. This project aimed to determine if pathogenic Pythium species are harbored in greenhouse recycled irrigation water tanks and to determine the ecology of the Pythium species found in these tanks. In previous research, an extensive water survey was performed on the recycled irrigation water tanks of two commercial greenhouses in Pennsylvania that experience frequent poinsettia crop loss due to Pythium aphanidermatum. In that work, only a preliminary identification of the baited species was made. Here, detailed analyses of the isolates were conducted. The Pythium and Phytopythium species recovered during the survey by baiting the water were identified and assessed for pathogenicity in lab and greenhouse experiments. The Pythium species found during the tank surveys were: a species genetically very similar to P. sp. nov. OOMYA1702-08 in Clade B2, two distinct species of unknown identity in Clade E2, P. -
Aisys CS² User's Reference Manual Software Revision 10.X User Responsibility
Aisys CS² User's Reference Manual Software Revision 10.X User responsibility Datex-Ohmeda, Inc. a General Electric Company, doing business as GE Healthcare. This product will perform in conformity with the description thereof contained in this User’s Reference manual and accompanying labels and/or inserts, when assembled, operated, maintained, and repaired in accordance with the instruction provided. This Product must be checked periodically. A defective Product should not be used. Parts that are broken, missing, plainly worn, distorted, or contaminated should be replaced immediately. Should repair or replacement become necessary, Datex-Ohmeda recommends that a telephonic or written request for service advice be made to the nearest Datex- Ohmeda Customer Service Center. This Product or any of its parts should not be repaired other than in accordance with written instructions provided by Datex-Ohmeda and by Datex-Ohmeda trained personnel. The Product must not be altered without the prior written approval of Datex-Ohmeda. The user of this Product shall have the sole responsibility for any malfunction which results from improper use, faulty maintenance, improper repair, damage, or alteration by anyone other than Datex-Ohmeda. CAUTION U.S. Federal law restricts this device to sale by or on the order of a licensed medical practitioner.Outside the U.S.A., check the local laws for any restriction that may apply. Table of Contents 1 Introduction Intended use .....................................1-2 Indications for use ..............................1-2 General information .............................1-2 Serial numbers .................................1-4 Trademarks ...................................1-5 Symbols used in the manual or on the equipment ........1-6 Symbols used on the equipment ...................1-6 Symbols used on the user interface ................1-9 Typeface conventions used ....................... -
Bioinformatic and Biostatitic Analysis of Epigenetic Data from Humans and Mice in the Context of Obesity and Its Complications Sarah Voisin
Bioinformatic and biostatitic analysis of epigenetic data from humans and mice in the context of obesity and its complications Sarah Voisin To cite this version: Sarah Voisin. Bioinformatic and biostatitic analysis of epigenetic data from humans and mice in the context of obesity and its complications. Development Biology. Université Pierre et Marie Curie - Paris 6; Uppsala University, 2016. English. tel-02800507 HAL Id: tel-02800507 https://hal.inrae.fr/tel-02800507 Submitted on 5 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1245 Bioinformatic and Biostatistic Analysis of Epigenetic Data from Humans and Mice in the Context of Obesity and its Complications SARAH VOISIN ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 UPPSALA ISBN 978-91-554-9655-5 2016 urn:nbn:se:uu:diva-300751 Dissertation presented at Uppsala University to be publicly examined in Uppsala, Thursday, 22 September 2016 at 13:00 for the degree of Doctor of Philosophy (Faculty of Medicine). The examination will be conducted in English. Faculty examiner: Associate professor Romain Barres (Section for Integrative Physiology, University of Copenhagen, Denmark). -
Carrot Cavity Spot
Factsheet 03/03 Horticultural Bradbourne House Development East Malling Council Kent ME19 6DZ Carrots T: 01732 848383 F: 01732 848498 Project No. FV 5a–f E: [email protected] Carrot cavity spot By Tim Pettitt, HRI Wellesbourne and Peter Gladders, ADAS Cavity spot of carrot, caused by slow-growing Pythium species, is currently the most economically important disease problem in UK carrot crops. Affected carrots, with only one or two visible lesions, are rejected at grading. When disease incidence in the field passes a relatively low threshold it becomes uneconomical to harvest crops. This means that virtually 100% control is necessary to avoid economic losses. In a severe cavity spot season, 15–20% or more of crops can be rejected by pack-houses. This amounts to an estimated loss of £10.2 –13.6 million based on the 2000–2001 value of the crop (DEFRA Horticultural Statistics, 2001). Although good control of the disease was achieved in the early 1980s with metalaxyl and related fungicides, there have recently been increasing problems in the management of cavity spot. This factsheet summarises recent HDC funded research and its application for management of the disease. Symptoms of cavity spot The appearance of cavities normally starts as small, pale, sunken elliptical spots, under an apparently intact outer skin. These lesions gradually darken in colour to a greyish brown and, depending on environmental conditions (see below), they may increase in size rapidly, or expand more slowly with the natural growth of the carrot root. Eventually, the outer skin ruptures, leaving an open cavity where the tissues underneath have been attacked by the fungus and secondary organisms. -
Management of Damping-Off Caused by Pythium Spp. in Organic
MANAGEMENT OF DAMPING-OFF CAUSED BY PYTHIUM SPP. IN ORGANIC VEGETABLE PRODUCTION IN THE PACIFIC NORTHWEST By ANA VIDA CRISOSTOMO ALCALA A thesis submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Plant Pathology JULY 2013 To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of ANA VIDA CRISOSTOMO ALCALA find it satisfactory and recommend that it be accepted. __________________________________ Lindsey du Toit, Ph.D., Chair __________________________________ Carol Miles, Ph.D. __________________________________ Tim Paulitz, Ph.D. __________________________________ Lyndon Porter, Ph.D. ii ACKNOWLEDGEMENTS Professional I am greatly indebted to four great scientists who mentored me in my PhD. My deepest gratitude is to Dr. Lindsey du Toit, my major advisor, for opening the door of opportunity for me to pursue my Ph.D. in the US, and for providing me with every chance to develop a variety of skills essential for this profession. Her enthusiasm, passion, and dedication to research have been inspirational to me. To my committee members, Dr. Carol Miles, Dr. Tim Paulitz, and Dr. Lyndon Porter, who generously took time to mentor me, by distance or whenever I got a chance to work on campus, as well as for generously sharing their expertise. To the very hardworking VSP crew: Mike, Barb, Sarah, John, and Anita, for all their help in one or many aspects of this project. Particularly to Mike, for his expertise and tremendous help in my field, greenhouse, and lab trials; Barb, for always being ready to help even beyond the call of duty, and for always making what seemed an impossible task possible. -
Role of Pythium Spp. in the Development of Cavity Spot on Carrot in the Fraser Valley of British Columbia
ROLE OF PYTHIUM SPP. IN THE DEVELOPMENT OF CAVITY SPOT ON CARROT IN THE FRASER VALLEY OF BRITISH COLUMBIA Dee Ann L. Benard B.Sc., Simon Fraser University, 1990 THESIS SUBMITTED IN PARTIAL FULFILLMI<NT 01: THE REQUIREMENTS FOR THE DEGREE OF . MASTER OF SCIENCE in the Department o f Biological Sciences O Dee Ann L. Benard 1994 SIMON FRASER UNIVERSITY May 1994 All rights reserved. This work may not be reproduced in whulc or in part, by photocopy or other mems, without permission of the author APPROVAL Name: DEE ANN LYNN BENARD Degree: Master of Science Title of Thesis: ROLE OF PYTFIIUM SPP. IN TIIE DEVELOPMENT OF CAVITY SPOT ON CARROTS IN TIIE FRASER VALLEY OF BRITISII COLUMBIA Examining Committee: Chair: Dr. R. Nicholsp, Associate Professor Dr. Z. K. Punja, Associate Pro'fesso ior Supervisor Department of Biological Sciences, V Sciences, SFU I Mr. D;-Urmrod, PMnt PathWagist ' B.C. Ministry of Agriculture, Fisheries and Food Public Examiner Date Approved /W?/~l(j-/// PARTIAL COPYRIGHT LICENSE I hereby grant to Simon Fraser University the right to lend my thesis, project or extended essay (the title of which is shown below) to users of the Simon Fraser University Library, and to make partial or single copies only for such users or in response to a request from the library of any other university, or other educational institution, on its own behalf or for one of its users. I further agree that permission for multiple copying of this work for scholarly purposes may be granted by me or the Dean of Graduate Studies. -
Diagnostic Tests and Their Application in the Management of Soil- and Water-Borne Oomycete Pathogen Species A.J
REVIEW ARTICLE Diagnostic tests and their application in the management of soil- and water-borne oomycete pathogen species A.J. Wakeham & T.R. Pettitt Institute for Science & the Environment, University of Worcester, Worcester, UK Keywords: disease management, diagnosis, crop pathogens, Correspondence A.J. Wakeham, Institute for Science & the Environment, Charles Darwin Building, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK Email: [email protected] Abstract Oomycete diseases cause significant losses across a broad range of crop and aquaculture commodities worldwide. These losses can be greatly reduced by disease management practices steered by accurate and early diagnoses of pathogen presence. Determinations of disease potential can help guide optimal crop rotation regimes, varietal selections, targeted control measures, harvest timings and crop post-harvest handling. Pathogen detection prior to infection can also reduce the incidence of disease epidemics. Classical methods for the isolation of oomycete pathogens are normally deployed only after disease symptom appearance. These processes are often-time consuming, relying on culturing the putative pathogen(s) and the availability of expert taxonomic skills for accurate identification; a situation that frequently results in either delayed application, or routine ‘blanket’ over- application of control measures. Increasing concerns about pesticides in the environment and the food chain, removal or restriction of their usage combined with rising costs have focussed interest in the development and improvement of disease management systems. To be effective, these require timely, accurate and preferably quantitatve diagnoses. A wide range of rapid diagnostic tools, from point of care immunodiagnostic kits to next generation nucleotide sequencing have potential application in oomycete disease management.