DOCSLIB.ORG

I. Introduction

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
I. Introduction République Algérienne Démocratique et Populaire Ministère de L’enseignement Supérieur et de la Recherche Scientifique Université Abdelhamid Ibn Badis – Mostaganem Faculté des Sciences de la Nature et de la Vie Département de Biologie THESE DE DOCTORAT Présentée par DILMI Fatiha Pour obtenir le diplôme de DOCTORAT EN SCIENCES Filière: Sciences Biologiques Spécialité: Microbiologie Moléculaire THEME ISOLEMENT ET CARACTÉRISATION DES MICRO ORGANISMES CAPABLE DE DEGRADER LE PETROLE DE LA RAFFINERIE D'ARZEW Soutenue publiquement le: 19 / 06 / 2019 devant le Jury composé de: Président MEKHALDI Abdelkader Prof Université Abdelhamid Ibn Badis – Mostaganem Examinateur DJIBAOUI Rachid Prof Université Abdelhamid Ibn Badis – Mostaganem Examinateur KIHAL Mebrouk Prof Université Oran 1 Ahmed Benbella Examinateur BOUHADDA Youcef Prof Université Mustapha Stambouli- Mascara Examinateur SENOUCI Khadidja MCA Université Mustapha Stambouli- Mascara Promoteur CHIBANI Abdelwaheb Prof Université Abdelhamid Ibn Badis – Mostaganem Laboratoire de Microbiologie et Biologie Végétale Année universitaire 2018-2019 People’s Democratic Republic of Algeria Ministry of higher Education and Scientific Research Abdelhamid Ibn Badis University – Mostaganem Faculty of Natural and Life Sciences Department of Biology DOCTORAL THESIS Presented by DILMI Fatiha For admittance to the degree of DOCTORATE IN SCIENCES Branch: Biological Sciences Specialty: Molecular Microbiology THEME ISOLATION AND CHARACTERIZATION OF OIL DEGRADING MICROORGANISMS FROM ARZEW OIL REFINERY Publicly Examined on : 19 / 06 / 2019 in front of the following examiners’ Committee Chairman MEKHALDI Abdelkader Prof University of Abdelhamid Ibn Badis – Mostaganem Examiner DJIBAOUI Rachid Prof University of Abdelhamid Ibn Badis – Mostaganem Examiner KIHAL Mebrouk Prof University of Oran 1 Ahmed Benbella Examiner BOUHADDA Youcef Prof University of Mustapha Stambouli- Mascara Examiner SENOUCI Khadidja MCA University of Mustapha Stambouli- Mascara Supervisor CHIBANI Abdelwaheb Prof University of Abdelhamid Ibn Badis – Mostaganem Laboratory of Microbiology and Plant Science University year 2018-2019 DEDICATIONS I dedicate this thesis to: My Mother Source of light of my life My Father God bless his age My husband for his help, supports, understanding and encouragement during my study My children Joumana, Anes and Raihana, source of happiness and love My brother and my sisters To all my family To all my friends I ACKNOWLEDGMENTS له الحمد في الﻷولى واﻵخرة First, I must express my deepest thanks to ALLAH. Without support and pity of ALLAH, I would have never been able to start and finish my thesis. I would like to express my deepest and sincere gratitude to my advisor Pr. CHIBANI Abdelwaheb, for his guidance, instruction and support throughout this research work. I would also like to thank my advisory committee, Pr. MEKHALDI Abdelkader, Pr. DJIBAOUI Rachid, Pr. KIHAL Mebrouk, Pr. BOUHADDA Youcef and Dr. SENOUCI Khadidja, for their constructive suggestions and comments. I immensely grateful to Pr. BOUHADDA Y, for allowing me to use his laboratory equipment‘s and for his kindness and help. I would like to thank Mr. DJENDARA A for his time and help. And also I would like to extend my gratitude to Dr Senouci k, for her support and help. Many thanks to thank Dr. LEPAGE Pierre and all the members of McGill University and Genome Québec Innovation Centre, Montreal Canada for their helpful material and comments. I would also like to thank Mr BEHIH and all members of National Institute of Soils, Irrigation and Drainage (INSID of Ksar Chellala, Algeria). Extra thanks to Mr. BELMIMOUNE A and all member of Arzew oil refinery. II ملخص حػد حظسباث البترول ومىخجاجه التي جددر أزىاء الىقل، الخخصًٍ والخكسٍس مً أبسش امللىزاث البيئيت هظسا للظسز الكبير الري جددزه في الىظام البيئي. وحػخبر املػالجت الحيىٍت باطخخدام الكائىاث الدقيقت طسٍقت فػالت ملػالجت التربت امللىزت بالىفط. تهدف هره الدزاطت الى غصل و حشخيص وجددًد البكخيرًا املدللت للىفط مً جسبت ملىزت بهرا ألاخير؛ وخﻻل هره الدزاطت جم جمؼ خمظت غشس غيىت مً التربت امللىزت بالىفط مً طبػت مىاقؼ في مصفاة أزشٍى، الكائىت شمال ؾسب الجصائس. وبمػاًىت الخصائص الفيزًائيت والكيميائيت لػيىاث التربت وجد أن السمل والطين هما الجصءان الظائدان فيها، وأنها جدخىي غلى وظبت ملىخت مىخفظت، وهي ملىزت بيظب غاليت 5 بمجمىع هيدزوكسبىهاث هفطيت جتراوح مً 2 إلى ؽ 68 / كلغ . في خين جساوح الخػداد البكخيري مً x 10 1.6 إلى 8 x 10 1.4 وخدة قادزة عى الىم ى لكل ؾسام واخد مً التربت مما ٌشير أنها جدخىي غلى حػداد بكخيري غا ٍل مقازهت مؼ التربت ؾير امللىزت. جم غصل 86 مظخػمسة بكخيرًت ذاث أحجام وألىان مخخلفت باطخخدام وطط مػدوي ًدخىي غلى 1٪ مً الىفط الخام. وقد جم اهخقاء وجددًد ازىين وغشسًٍ طﻻلت بكخيرًت بالىظسالى قدزتها الػاليت غلى جدليل الىفط الخام، ومً زم جددًدها مً خﻻل الخصائص املسفىلىجيت و البيى كيميائيت. وكاهذ 11 طﻻلت بكخيرًت فقط مىطىع الخىصيف الجصٍئي، وذلك وفقا لطــسٍقت الدظلظل الجيني ملىززت الحمع الىىوي السٍبي ARNr 18S و قد وصفذ الظﻻﻻث البكخيرًت املػصولت غلى أنها ألاجىاض و / أو ألاهىاع الخاليت : Pseudomonas aeruginosa, Achromobacter xylosoxidans, Staphylococcus haemolyticus, Enterococcus faecalis, Bacillus cereus, B. anthracis, B. subtilis, Exiguobacterium aurantiacum, و Lysinibacillus macroides, P. fluorescens, Burkholderia cepacia, Staphylococcus hominis Lysinibacillus sphaericus. في خين أبدث 6 طﻻﻻث بكخيرًت مً هىع P. aeruginosa هديجت إًجابيت مؼ البادئت ألاولى املطابقت للمىززت 434bp) alkane 1 monoxygenase)، وقد جم اخخباز قدزة 12 طﻻلت مػصولت غلى جدليل الىفط في وطط مػدوي مً خﻻل قياض الكثافت الظىئيت والخدليل الكخلي. خيث أشازث الىخائج إلى أن جميؼ الظﻻﻻث املػصولت لها القدزة غلى اطخخدام الىفط الخام كمصدز وخيد للكسبىن . كما لىخظ أن أغلى مػدل همى كان لدي طﻻﻻث P2.1( Pseudomonas aeruginosa وB4.2 Lysinibacillus macroides ،)P2.3 و P2.2 Achromobacter xylosoxidans وهي الظﻻﻻث هفظها التي خققذ أغلى مظخىٍاث الخدليل البيىلىجي، بديث جاءث وظبها غلى الخىالي %76.37، %60.92، %47.46 و45.20% . ومً جاهب آخس جم اخخباز قدزة الظﻻ ﻻث املػصولت )مىفسدة ومجخمػت( غلى جدليل الدًصل مً خﻻل قياض الكثافت الظىئيت،الخدليل الكخلي وجدليل GC-MS. وقد دلذ الىخائـــــــج غلى أن أغلى مظخىٍاث الىمى في وطط مػدوي مصود بالدًصل كان لدي املجمؼ البكخيري وطﻻلت Pseudomonas aeruginosa P2.1. وأن أغلى مػدﻻث الخدليل البيىلىجي كاهذ للمجمؼ البكخيري بيظبت 86.82٪ وجليها طﻻلت Pseudomonas aeruginosa P2.1 بيظبت 88.61٪، وخلصذ الىخائج أن لدي املجمؼ البكخيري قدزة غاليت غلى الخدليل البيىلىجي للدًصل مقازهت بالظﻻﻻث الفسدًت، بيىما كشف جدليل GC-MS أن املجمؼ البكخيري والظﻻﻻث الفسدًت ًدلﻻن بشكل أكبر الجصء ألاليفاحي للدًصل مقازهت بالجصء الػطسي وأن هىاك اهخفاض في جل مسكباث III الدًصل و بشكل خاص غىد اطخخدام الخجمؼ البكخيري وجد أن هىاك اهخفاض كلي ملسكباث n-alkane )مً C9 إلى C26( وهرا بػد 11 ًىما مً الخدظين. وأخيرا جم جددًد الظسوف املثلى )دزجت الحسازة و دزجت الحمىطت و امللىخت و التهىٍت( التي جمىذ الظﻻﻻث البكخيرًت قدزة غاليت غلى الخدليل البيىلىجي للىفط. خلصذ الدزاطت إلى أن غيىاث التربت املدزوطت جدخىي غلى مجمىغت مخىىغت مً البكخيرًا املدطمت للىفط وٍمكً اطخخدام هره الظﻻﻻث في املػالجت الحيىٍت للتربت امللىزت بالىفط والىفاًاث الىفطيت ألاخسي. الكلمات املفتاحية: الػصل، الخىصيف، الخدليل البيىلىجي، الكائىاث الحيت الدقيقت، الىفط الخام، الدًصل، حظلظل الجين 18S ARNr ، التربت امللىزت بالىفط ، مصفاة أزشٍ ى الىفطيت. IV ABSTRACT The spills of petroleum and petroleum product, which occur during transport, storage and refining, are a major contaminant in the environment, as they produce harm to the surrounding ecosystem. Bioremediation is an efficient method used to treat petroleum hydrocarbon contaminated soil using indigenous microorganisms. The purpose of our study was to isolate, screen and identify the hydrocarbon degrading bacteria from oil polluted soil. Fifteen Oil-contaminated soil samples were aseptically collected from seven sites in Arzew oil refinery, North-West of Algeria. Physico- chemical parameters of soil samples showed that sand and loam were the predominant fractions. The soils were neutral to slightly alkaline pH, have a low salinity and highly polluted with total hydrocarbon content ranging from 2 to 86 g/kg soil. Bacterial enumeration ranged from 1.6 x 105 to 1.4 x 108 CFU/g soil indicating high bacterial count in oil-contaminated soils compared with non-contaminated one. Seventy-eight bacterial colonies with different size and color were isolated using mineral salt media supplemented with 1% of crude oil. Twenty-two bacterial isolates were screened for their best degradative abilities of crude oil, and then they were identified based on morphological and biochemical characterizations. Fifteen isolates were identified using 16S rRNA gene sequence analysis; the isolates were identified as the following genera and/or species: Pseudomonas aeruginosa, Achromobacter xylosoxidans, Staphylococcus haemolyticus, Enterococcus faecalis, Bacillus cereus, B. anthracis, B. subtilis, Exiguobacterium aurantiacum, Lysinibacillus macroides, P. fluorescens, Burkholderia cepacia, Staphylococcus hominis and Lysinibacillus sphaericus. Six bacterial isolates ( identified as P. aeruginosa) showed a positive result with primer pair specific to alkane 1 monoxygenase gene (434bp). The ability of 12 isolated strains to degrade crude oil was carried out in a liquid medium by measuring optical density and gravimetric analysis. Results indicated that all the isolated strains had effectively utilized crude oil as carbon source. Pseudomonas aeruginosa (P2.1 and P2.3), Lysinibacillus macroides B4.2 and Achromobacter xylosoxidans P2.2 had the highest growth in the medium with crude oil and exhibited the highest biodegradation percentage with 76.37%, 60.92%, 47.46% and 45.20% respectively. The ability of individual pure isolates and bacterial
Load more

Recommended publications
  • Intramammary Infections with Coagulase-Negative Staphylococcus Species
    Printing of this thesis was financially supported by Printed by University Press, Zelzate ISBN number: 9789058642738 INTRAMAMMARY INFECTIONS WITH COAGULASE-NEGATIVE STAPHYLOCOCCUS SPECIES IN BOVINES - MOLECULAR DIAGNOSTICS AND EPIDEMIOLOGY - KARLIEN SUPRÉ 2011 PROMOTORS/PROMOTOREN Prof. dr. Sarne De Vliegher Faculteit Diergeneeskunde, UGent Prof. dr. Ruth N. Zadoks Royal (Dick) School of Veterinary Studies, University of Edinburgh; Moredun Research Institute, Penicuik, Schotland Prof. dr. Freddy Haesebrouck Faculteit Diergeneeskunde, UGent MEMBERS OF THE EXAMINATION COMMITTEE/LEDEN VAN DE EXAMENCOMMISSIE Prof. dr. dr. h. c. Aart de Kruif Voorzitter van de examencommissie Prof. dr. Mario Vaneechoutte Faculteit Geneeskunde en Gezondheidswetenschappen, UGent Dr. Margo Baele Directie Onderzoeksaangelegenheden, UGent Dr. Lic. Luc De Meulemeester MCC-Vlaanderen, Lier Prof. dr. Geert Opsomer Faculteit Diergeneeskunde, UGent Prof. dr. Marc Heyndrickx Instituut voor Landbouw en Visserijonderzoek (ILVO), Melle Dr. Suvi Taponen University of Helsinki, Finland Prof. dr. Ynte H. Schukken Cornell University, Ithaca, USA INTRAMAMMARY INFECTIONS WITH COAGULASE-NEGATIVE STAPHYLOCOCCUS SPECIES IN BOVINES - MOLECULAR DIAGNOSTICS AND EPIDEMIOLOGY - KARLIEN SUPRÉ Department of Reproduction, Obstetrics, and Herd Health Faculty of Veterinary Medicine, Ghent University Dissertation submitted in the fulfillment of the requirements for the degree of Doctor in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University INTRAMAMMAIRE INFECTIES MET COAGULASE-NEGATIEVE
    [Show full text]
  • Molecular Diversity and Multifarious Plant Growth
    Environment Health Techniques 44 Priyanka Verma et al. Research Paper Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India Priyanka Verma1,2, Ajar Nath Yadav1, Kazy Sufia Khannam2, Sanjay Kumar3, Anil Kumar Saxena1 and Archna Suman1 1 Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India 2 Department of Biotechnology, National Institute of Technology, Durgapur, India 3 Division of Genetics, Indian Agricultural Research Institute, New Delhi, India The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19–27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, andStaphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia).
    [Show full text]
  • Elucidation of Spatiotemporal Variations in Functional Genes Involved in the Nitrogen Cycle Along the West Coast of India
    Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India A thesis submitted to Goa University for the award of degree of Doctor of Philosophy In MICROBIOLOGY By JASMINE GOMES Under the guidance of Dr. RAKHEE KHANDEPARKER Senior Scientist Biological Oceanography Division CSIR-National Institute of Oceanography Dona Paula-Goa 403004 April 2018 CERTIFICATE Certified that the research work embodied in this thesis entitled ―Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India‖ submitted by Ms. Jasmine Gomes for the award of Doctor of Philosophy degree in Microbiology at Goa University, Goa, is the original work carried out by the candidate himself under my supervision and guidance. Dr. Rakhee Khandeparker Senior Scientist Biological Oceanography Division CSIR-National Institute of Oceanography, Dona Paula – Goa 403004 DECLARATION As required under the University ordinance, I hereby state that the present thesis for Ph.D. degree entitled ―Elucidation of spatiotemporal variations in functional genes involved in the nitrogen cycle along the west coast of India" is my original contribution and that the thesis and any part of it has not been previously submitted for the award of any degree/diploma of any University or Institute. To the best of my knowledge, the present study is the first comprehensive work of its kind from this area. The literature related to the problem investigated has been cited. Due acknowledgement have been made whenever facilities and suggestions have been availed of. JASMINE GOMES Acknowledgment I take this privilege to express my heartfelt thanks to everyone involved to complete my Ph.D successfully.
    [Show full text]
  • Alves Simões, Patrícia Belinda (2018) Intramammary Infection in Heifers – the Application of Infrared Thermography As an Early Diagnostic Tool
    Alves Simões, Patrícia Belinda (2018) Intramammary infection in heifers – the application of infrared thermography as an early diagnostic tool. MVM(R) thesis. https://theses.gla.ac.uk/30801/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Intramammary infection in heifers – the application of infrared thermography as an early diagnostic tool Patrícia Belinda Alves Simões IMVM MRCVS Submitted in fulfilment of the requirements for the Degree of Masters of Veterinary Medicine School of Veterinary Medicine College of Medical, Veterinary & Life Sciences University of Glasgow September 2018 2 Abstract Mastitis is mainly caused by intramammary infection (IMI) with bacteria. Heifer IMI in early lactation impacts negatively on welfare, milk production and longevity in the herd. Prevention of subclinical and clinical mastitis caused by IMI with major pathogens, such as Streptococcus uberis and Staphylococcus aureus, could be improved if more information about the origin of heifer IMI were available. The challenges of establishing when in the pre- or peri-partum period the infection occurs make targeting of preventive management difficult.
    [Show full text]
  • Advancements in the Understanding of Staphylococcal
    ADVANCEMENTS IN THE UNDERSTANDING OF STAPHYLOCOCCAL MASTITIS THROUGH THE USE OF MOLECULAR TOOLS __________________________________________ A Dissertation presented to the Faculty of the Graduate School at the University of Missouri-Columbia __________________________________________ In partial fulfillment of the requirements for the degree Doctor of Philosophy __________________________________________ By PAMELA RAE FRY ADKINS Dr. John Middleton, Dissertation Supervisor May 2017 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled ADVANCEMENTS IN THE UNDERSTANDING OF STAPHYLOCOCCAL MASTITIS THROUGH THE USE OF MOLECULAR TOOLS presented by Pamela R. F. Adkins, a candidate for the degree of Doctor of Philosophy, and hereby certify that, in their opinion, it is worthy of acceptance. Professor John R. Middleton Professor James N. Spain Professor Michael J. Calcutt Professor George C. Stewart Professor Thomas J. Reilly DEDICATION I dedicate this to my husband, Eric Adkins, and my mother, Denice Condon. I am forever grateful for their eternal love and support. ACKNOWLEDGEMENTS I thank John R. Middleton, committee chair, for this support and guidance. I sincerely appreciate his mentorship in the areas of research, scientific writing, and life in academia. I also thank all the other members of my committee, including Michael Calcutt, George Stewart, James Spain, and Thomas Reilly. I am grateful for their guidance and expertise, which has helped me through many aspects of this research. I thank Simon Dufour (University of Montreal), Larry Fox (Washington State University) and Suvi Taponen (University of Helsinki) for their contribution to this research. I acknowledge Julie Holle for her technical assistance, for always being willing to help, and for being so supportive.
    [Show full text]
  • PPPHE 2013 Endophytes for Plant Protection
    Persistent Identifier: urn:nbn:de:0294-sp-2013-ppphe-2 DPG Spectrum Phytomedizin C. Schneider, C. Leifert, F. Feldmann (eds.) Endophytes for plant protection: the state of the art Proceedings of the 5th International Symposium on Plant Protection and Plant Health in Europe held at the Faculty of Agriculture and Horticulture (LGF), Humboldt University Berlin, Berlin-Dahlem, Germany, 26-29 May 2013 jointly organised by the Deutsche Phytomedizinische Gesellschaft - German Society for Plant Protection and Plant Health (DPG) and the COST Action FA 1103 in co-operation with the Faculty of Agriculture and Horticulture (LGF), Humboldt University Berlin, and the Julius Kühn-Institut (JKI), Berlin, Germany Publisher Persistent Identifier: urn:nbn:de:0294-sp-2013-ppphe-2 Bibliografische Information der Deutschen Bibliothek Die Deutsche Bibliothek verzeichnet diese Publikation in der Deutschen Nationalbibliografie; Detaillierte bibliografische Daten sind im Internet über http://dnb.ddb.de abrufbar. ISBN: 978-3-941261-11-2 Das Werk einschließlich aller Teile ist urheberrechtlich geschützt. Jede kommerzielle Verwertung außerhalb der engen Grenzen des Urheberrechtsgesetzes ist ohne Zustimmung der Deutschen Phytomedizinischen Gesellschaft e.V. unzulässig und strafbar. Das gilt insbesondere für Vervielfältigungen, Übersetzungen, Mikroverfilmungen und die Einspeicherung und Verarbeitung in elektronischen Systemen. Die DPG gestattet die Vervielfältigung zum Zwecke der Ausbildung an Schulen und Universitäten. All rights reserved. No part of this publication may be reproduced for commercial purpose, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the copyright owner. DPG allows the reproduction for education purpose at schools and universities.
    [Show full text]
  • Subklinik Mastitisli Keçilerden Izole Edilen Stafilokok Türlerinin Farkli Virulens
    T.C. AYDIN ADNAN MENDERES ÜNİVERSİTESİ SAĞLIK BİLİMLERİ ENSTİTÜSÜ MİKROBİYOLOJİ YÜKSEK LİSANS PROGRAMI SUBKLİNİK MASTİTİSLİ KEÇİLERDEN İZOLE EDİLEN STAFİLOKOK TÜRLERİNİN FARKLI VİRULENS ÖZELLİKLERİNİN ARAŞTIRILMASI EVRİM DÖNMEZ YÜKSEK LİSANS TEZİ DANIŞMAN Prof. Dr. Şükrü KIRKAN Bu tez Aydın Adnan Menderes Üniversitesi Bilimsel Araştırma Projeleri Birimi tarafından VTF-19034 proje numarası ile desteklenmiştir. AYDIN–2020 KABUL VE ONAY SAYFASI T.C. Aydın Adnan Menderes Üniversitesi Sağlık Bilimleri Enstitüsü Mikrobiyoloji Anabilim Dalı Yüksek Lisans Programı çerçevesinde Evrim DÖNMEZ tarafından hazırlanan “Subklinik Mastitisli Keçilerden İzole Edilen Stafilokok Türlerinin Farklı Virulens Özelliklerinin Araştırılması” başlıklı tez, aşağıdaki jüri tarafından Yüksek Lisans Tezi olarak kabul edilmiştir. Tez Savunma Tarihi: 26/08/2020 Aydın Adnan ....………. Üye (T.D.) : Prof. Dr. Şükrü KIRKAN Menderes Ünivesitesi İstanbul Üniversitesi- ....………. Üye : Prof. Dr. Serkan İKİZ Cerrahpaşa Aydın Adnan ....………. Üye : Doç. Dr. Uğur PARIN Menderes Üniversitesi ONAY: Bu tez Aydın Adnan Menderes Üniversitesi Lisansüstü Eğitim-Öğretim ve Sınav Yönetmeliğinin ilgili maddeleri uyarınca yukarıdaki jüri tarafından uygun görülmüş ve Sağlık Bilimleri Enstitüsünün ……………..……..… tarih ve ………………………… sayılı oturumunda alınan …………………… nolu Yönetim Kurulu kararıyla kabul edilmiştir. Prof. Dr. Süleyman AYPAK Enstitü Müdürü V. i TEŞEKKÜR Bu çalışmanın gerçekleştirilmesinde, değerli bilgilerini benimle paylaşan, bana kıymetli zamanını ayırıp büyük bir ilgi ve sabırla bana faydalı olabilmek için elinden geleni sunan kıymetli danışman hocam Prof. Dr. Sükrü KIRKAN’a teşekkürü bir borç biliyorum. Yine çalışmamda konu, kaynak ve yöntem açısından bana sürekli yardımda bulunarak yol gösteren her sorun yaşadığımda yanına çekinmeden gidebildiğim, güler yüzünü ve samimiyetini benden esirgemeyen Arş. Gör. Dr. Hafize Tuğba YÜKSEL DOLGUN’a de sonsuz teşekkürlerimi sunarım. Teşekkürlerin az kalacağı hocalarım Prof. Dr. K. Serdar DİKER’e, Prof.
    [Show full text]
  • Review Memorandum
    510(k) SUBSTANTIAL EQUIVALENCE DETERMINATION DECISION SUMMARY A. 510(k) Number: K181663 B. Purpose for Submission: To obtain clearance for the ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel C. Measurand: Bacillus cereus group, Bacillus subtilis group, Corynebacterium, Cutibacterium acnes (P. acnes), Enterococcus, Enterococcus faecalis, Enterococcus faecium, Lactobacillus, Listeria, Listeria monocytogenes, Micrococcus, Staphylococcus, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Streptococcus, Streptococcus agalactiae (GBS), Streptococcus anginosus group, Streptococcus pneumoniae, Streptococcus pyogenes (GAS), mecA, mecC, vanA and vanB. D. Type of Test: A multiplexed nucleic acid-based test intended for use with the GenMark’s ePlex instrument for the qualitative in vitro detection and identification of multiple bacterial and yeast nucleic acids and select genetic determinants of antimicrobial resistance. The BCID-GP assay is performed directly on positive blood culture samples that demonstrate the presence of organisms as determined by Gram stain. E. Applicant: GenMark Diagnostics, Incorporated F. Proprietary and Established Names: ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel G. Regulatory Information: 1. Regulation section: 21 CFR 866.3365 - Multiplex Nucleic Acid Assay for Identification of Microorganisms and Resistance Markers from Positive Blood Cultures 2. Classification: Class II 3. Product codes: PAM, PEN, PEO 4. Panel: 83 (Microbiology) H. Intended Use: 1. Intended use(s): The GenMark ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a qualitative nucleic acid multiplex in vitro diagnostic test intended for use on GenMark’s ePlex Instrument for simultaneous qualitative detection and identification of multiple potentially pathogenic gram-positive bacterial organisms and select determinants associated with antimicrobial resistance in positive blood culture.
    [Show full text]
  • Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
    Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances.
    [Show full text]
  • Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus Aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis
    foods Article Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis Ana G. Abril 1 ,Mónica Carrera 2,* , Karola Böhme 3, Jorge Barros-Velázquez 4 , Benito Cañas 5, José-Luis R. Rama 1, Tomás G. Villa 1 and Pilar Calo-Mata 4,* 1 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; [email protected] (A.G.A.); [email protected] (J.-L.R.R.); [email protected] (T.G.V.) 2 Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain 3 Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain; [email protected] 4 Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain; [email protected] 5 Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain; [email protected] * Correspondence: [email protected] (M.C.); [email protected] (P.C.-M.) Abstract: The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant Citation: Abril, A.G.; Carrera, M.; peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal Böhme, K.; Barros-Velázquez, J.; peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, Cañas, B.; Rama, J.-L.R.; Villa, T.G.; structural phage proteins, uncharacterized phage proteins and complement inhibitors.
    [Show full text]
  • Documento Completo.Pdf
    Universidad Nacional de La Plata Facultad de Ciencias Veterinarias Tesis de Doctorado Mastitis bovina causada por Staphylococcus coagulasa negativos Cesar Celestino Bonetto 2014 UNIVERSIDAD NACIONAL DE LA PLATA FACULTAD DE CIENCIAS VETERINARIAS Trabajo de Tesis realizado como requisito para optar el título de DOCTOR EN CIENCIAS VETERINARIAS Mastitis bovina causada por Staphylococcus coagulasa negativos Autor: BONETTO, Cesar Celestino Director: Doctora Claudia G. Raspanti Co-director: Doctora Gabriela I. Giacoboni Lugar de trabajo: Laboratorio de Genetica Microbiana Dpto. de Microbiologia e Inmunologia Facultad de Ciencias Exactas, Físico Químicas y Naturales. Universidad Nacional de Rio Cuarto. Laboratorio Labvima S.H Villa Maria–Córdoba Miembros del Jurado: Doctora Mercedes Lojo Doctora Nora Mestorino Doctor Luis Calvhino 2014 I A mi esposa e hijos por su paciencia y comprensión II AGRADECIMIENTOS A la Universidad Nacional de La Plata por haberme permitido obtener mi titulo de Posgrado A la Universidad Nacional de Río Cuarto por haberme permitido desarrollar el trabajo de Tesis. A la Dra. Claudia Raspanti por brindar su conocimiento y experiencia en mi formación científica e intelectual, además su valiosa predisposición y generosidad. A la Dra. Grabiela Giacoboni por su permanente apoyo, estímulo y colaboración. A la Dra. Nora Mestorino, Dra. Mercedes Lojo, Dr Luis Calvinho, por haber aceptado ser tribunal de esta Tesis y por sus aportes científicos a la misma. A todos los integrantes del Laboratorio de Genética Microbiana de la UNRC por los momentos compartidos. A la Dra. Cristina Bogni, Dra. Liliana Odierno, Dra. Claudina Vissio y Dr. Alejandro Larriestra, por su aporte en este trabajo de Tesis. A mi familia por su inagotable acompañamiento.
    [Show full text]
  • 1.5 M Wide from Furrow to Furrow), Followed by Feather Meal (12 − 0 − 0) Banded in at a Rate of 40 Kg N Ha− 1
    Supplemental Material Field trial preparation and sampling Field preparation included spading and bed formation (1.5 m wide from furrow to furrow), followed by feather meal (12 − 0 − 0) banded in at a rate of 40 kg N ha− 1. Experimental plots were established in eight experimental beds with rows of buffer plants between each experimental bed. Transplants were grown in the Westside Transplant facility in Winters, CA. After 9 wk. under certified organic management, seedlings were transplanted on the bed center by hand on 28 April 2019, followed by 1.9 cm of water applied via a single surface drip line in the center of each bed. Transplants that died due to a fungal blight (~100 plants) were replaced in the first three weeks of the experiment. Soil samples were taken at three depths (0-15cm, 15-30cm, 30-60cm) at transplant, mid- season (52 days after transplant) and harvest (116 days after transplant). Growth chamber experiments Seeds were sterilized by swirling in 2.7% bleach for 20 minutes, then washed 3 times with sterile water. 4 seeds per plate were germinated on 1% water agar. Plates were wrapped in aluminum foil for 7 days and stored at 21°C. After 1 week, plants were transferred to individual pots containing Sunshine #4 potting mix, where they were maintained at a 15 h day:9 h night light cycle. When plants were three weeks old, field communities were used to generate inocula. 4 Each sample from the field was divided in half, then diluted to 10 CFU/mL in 10 mM MgCl2.
    [Show full text]