Characterization and Biological Activity of Bacterial Glycoconjugates in Cold Adaptation
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Ecology and Epidemiology of Campylobacter Jejuni in Broiler Chickens
Ecology and Epidemiology of Campylobacter jejuni in Broiler Chickens A DISSERTATION SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Hae Jin Hwang IN PARTIALL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Dr. Randall Singer, Dr. George Maldonado June 2019 © Hae Jin Hwang, 2019 Acknowledgements I would like to sincerely thank my advisor, Dr. Randall Singer, for his intellectual guidance and support, great patience, and mentorship, which made this dissertation possible. I would also like to thank Dr. George Maldonado for his continuous encouragement and support. I would further like to thank my thesis committee, Dr. Richard Isaacson and Dr. Timothy Church, for their guidance throughout my doctoral training. I thank all my friends and colleagues I met over the course of my studies. I am especially indebted to my friends, Dr. Kristy Lee, Dr. Irene Bueno Padilla, Dr. Elise Lamont, Madhumathi Thiruvengadam, Dr. Kaushi Kanankege and Dr. Sylvia Wanzala, for their support and friendship. Heartfelt gratitude goes to my family, for always believing in me, encouraging me and helping me get through the difficult and stressful times during my studies. Lastly, I thank Sven and Bami for being the best writing companions I could ever ask for. i Abstract Campylobacteriosis, predominantly caused by Campylobacter jejuni, is a common, yet serious foodborne illness. With consumption and handling of poultry products as the most important risk factor of campylobacteriosis, reducing Campylobacter contamination in poultry products is considered the best public health intervention to reduce the burden and costs associated with campylobacteriosis. To this end, there is a need to improve our understanding of epidemiology and ecology of Campylobacter jejuni in poultry. -
Thèses Traditionnelles
UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Manuscript III
Manuscript III 60 Manuscript Initial characterization of ParI, an orphan C5-DNA methyltransferase from Psychrobacter arcticus 273-4 Miriam Grgic1, Gro Elin Kjæreng Bjerga2, Adele Kim Williamson1, Bjørn Altermark1 and Ingar Leiros1 1Department of chemistry, University of Tromsø, The Arctic University of Norway, Tromsø, Norway 2 University of Bergen, Bergen, Norway 1 Abstract Background DNA methyltransferase are important enzymes in most living organisms, from single cell bacteria to eukaryotes. In prokaryotes, most DNA methyltransferases are members of the bacterial type II restriction modification system: The DNA methyltransferases methylates host DNA, thereby protecting it from cleavage by the restriction endonucleases that recognize the same sequence. In addition to being part of restriction modification systems, DNA methyltransferases can act as orphan enzymes having important role in controlling gene expression, DNA replication, cell cycle and DNA post replicative mismatch repair. In higher eukaryotes, DNA methylation is involved in the regulation of gene expression, maintenance of genome integrity, parental imprinting, chromatin condensation as well as being involved in development of diseases and disorders. DNA-MTases have several potential applications in biotechnology for example in targeted gene silencing and in DNA-protein interaction studies Results According to bioinformatical analyses, the parI gene from Psychrobacter arcticus 273-4, encoding a cytosine specific DNA methyltransferase, is likely of phage origin. In this work, ParI was expressed and purified in a McrBC negative E. coli strain in fusion with a hexahistidine affinity tag and maltose binding protein solubility protein. The obtained recombinant ParI was monomeric with a molecular mass estimated to 54 kDa. The melting temperature of the protein was determined to be 53 ºC in ThermoFlour assay and 54 ºC in differential scanning calorimetry, with no secondary structures detectable at 65 ºC. -
Distribution of Bacteria in Lake Qarun, AL Fayoum, Egypt (2014 -2015) in Relation to Its Physical and Hydrochemical Characterization
Journal of Bioscience and Applied Research , 2016Vol.2, No.9, PP.601-615 pISSN: 2356-9174, eISSN: 2356-9182 601 Journal of Bioscience and Applied Research WWW.JBSAR.com Distribution of bacteria in Lake Qarun, AL Fayoum, Egypt (2014 -2015) in relation to its physical and hydrochemical characterization Mohamed Tawfiek Shaaban1, Hassan A.H. Ibrahim2, Amer Ahmed Mohammed Hanafi3 Botany Department, Faculty of Science, Menoufia University1,3; National Institute of Oceanography and Fisheries (NIOF), Alexandria2, Egypt (Corresponding author email : [email protected]) Abstract The bacteriological monitoring of Lake Qarun water and forty-five meters below sea level into the lowest, northern sediment (aerobic heterotrophs, Staphylococcus sp., Vibrio section of El- Fayoum Depression, Egypt. Although Lake sp. Aeromonas sp., S. feacalis, E. coli, and total coliform Qarun designated as protected area back in 1989, the Lake sp.) through the period of study (2014-2015) was carried has hardly been protected from various polluting elements. out. Six common bacterial isolates were fully identified as; It suffers from a serious water pollution problem which is Bacillus firmus, Bacillus stratosphericus, Exiguobacterium due to uncontrolled solid and liquid domestic and industrial mexicanum, Stenotrophomonas rhizophila, Halomonas waste disposal practices, in addition to agrochemical stevensii, and Halomonas korlensis based on partial contamination and lack of sustainable wastewater sequencing of 16Sr DNA. In addition, physical and management. Many fish farms were established around this chemical analyses of Lake Qarun water and sediment (pH, Lake (Mansour and Sidky, 2003). The Lake suffered drastic temperature, salinity, dissolved oxygen, BOD, COD, and chemical changes during the last years where it is used as a nutrients) were estimated. -
2011 Book Bacteriallipopolysa
Yuriy A. Knirel l Miguel A. Valvano Editors Bacterial Lipopolysaccharides Structure, Chemical Synthesis, Biogenesis and Interaction with Host Cells SpringerWienNewYork Yuriy A. Knirel Miguel A. Valvano N.D. Zelinsky Institute of Centre for Human Immunology and Organic Chemistry Department of Microbiology and Immunology Russian Academy of Sciences University of Western Ontario Leninsky Prospekt 47 London, ON N6A 5C1 119991 Moscow, V-334 Canada Russia [email protected] [email protected] This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying machines or similar means, and storage in data banks. Product Liability: The publisher can give no guarantee for all the information contained in this book. The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. # 2011 Springer-Verlag/Wien SpringerWienNewYork is a part of Springer Science+Business Media springer.at Cover design: WMXDesign GmbH, Heidelberg, Germany Typesetting: SPi, Pondicherry, India Printed on acid-free and chlorine-free bleached paper SPIN: 12599509 With 65 Figures Library of Congress Control Number: 2011932724 ISBN 978-3-7091-0732-4 e-ISBN 978-3-7091-0733-1 DOI 10.1007/978-3-7091-0733-1 SpringerWienNewYork Preface The lipopolysaccharide (LPS) is the major component of the outer leaflet of the outer membrane of Gram-negative bacteria. It contributes essentially to the integrity and stability of the outer membrane, represents an effective permeability barrier towards external stress factors, and is thus indispensable for the viability of bacteria in various niches, including animal and plant environment. -
Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment
RESEARCH ARTICLE Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment Christophe Leboulanger1*, HeÂlène Agogue 2☯, CeÂcile Bernard3☯, Marc Bouvy1☯, Claire Carre 1³, Maria Cellamare3¤³, Charlotte Duval3³, Eric Fouilland4☯, Patrice Got4☯, Laurent Intertaglia5³, CeÂline Lavergne2³, Emilie Le Floc'h4☯, CeÂcile Roques4³, GeÂrard Sarazin6☯ a1111111111 1 UMR MARBEC, Institut de Recherche pour le DeÂveloppement, Sète-Montpellier, France, 2 UMR LIENSs, Centre National de la Recherche Scientifique, La Rochelle, France, 3 UMR MCAM, MuseÂum National a1111111111 d'Histoire Naturelle, Paris, France, 4 UMR MARBEC, Centre National de la Recherche Scientifique, Sète- a1111111111 Montpellier, France, 5 Observatoire OceÂanologique de Banyuls-sur-Mer, Universite Pierre et Marie Curie, a1111111111 Banyuls-sur-Mer, France, 6 UMR7154 Institut de Physique du Globe de Paris, Universite Paris Diderot, a1111111111 Paris, France ☯ These authors contributed equally to this work. ¤ Current address: Phyto-Quality, 15 rue PeÂtrarque, Paris, France ³ These authors also contributed equally to this work. * [email protected] OPEN ACCESS Citation: Leboulanger C, Agogue H, Bernard C, Bouvy M, Carre C, Cellamare M, et al. (2017) Abstract Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical This study describes, for the first time, the water chemistry and microbial diversity in Dziani Thalassohaline Environment. PLoS ONE 12(1): e0168879. doi:10.1371/journal.pone.0168879 Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6± Editor: Jean-FrancËois Humbert, INRA, FRANCE -1 2- 14.5 g L eq. -
Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In
Table S8. Species identified by random forests analysis of shotgun sequencing data that exhibit significant differences in their representation in the fecal microbiomes between each two groups of mice. (a) Species discriminating fecal microbiota of the Soil and Control mice. Mean importance of species identified by random forest are shown in the 5th column. Random forests assigns an importance score to each species by estimating the increase in error caused by removing that species from the set of predictors. In our analysis, we considered a species to be “highly predictive” if its importance score was at least 0.001. T-test was performed for the relative abundances of each species between the two groups of mice. P-values were at least 0.05 to be considered statistically significant. Microbiological Taxonomy Random Forests Mean of relative abundance P-Value Species Microbiological Function (T-Test) Classification Bacterial Order Importance Score Soil Control Rhodococcus sp. 2G Engineered strain Bacteria Corynebacteriales 0.002 5.73791E-05 1.9325E-05 9.3737E-06 Herminiimonas arsenitoxidans Engineered strain Bacteria Burkholderiales 0.002 0.005112829 7.1580E-05 1.3995E-05 Aspergillus ibericus Engineered strain Fungi 0.002 0.001061181 9.2368E-05 7.3057E-05 Dichomitus squalens Engineered strain Fungi 0.002 0.018887472 8.0887E-05 4.1254E-05 Acinetobacter sp. TTH0-4 Engineered strain Bacteria Pseudomonadales 0.001333333 0.025523638 2.2311E-05 8.2612E-06 Rhizobium tropici Engineered strain Bacteria Rhizobiales 0.001333333 0.02079554 7.0081E-05 4.2000E-05 Methylocystis bryophila Engineered strain Bacteria Rhizobiales 0.001333333 0.006513543 3.5401E-05 2.2044E-05 Alteromonas naphthalenivorans Engineered strain Bacteria Alteromonadales 0.001 0.000660472 2.0747E-05 4.6463E-05 Saccharomyces cerevisiae Engineered strain Fungi 0.001 0.002980726 3.9901E-05 7.3043E-05 Bacillus phage Belinda Antibiotic Phage 0.002 0.016409765 6.8789E-07 6.0681E-08 Streptomyces sp. -
FINAL REPORT.Pdf
© FITRI BUDIYANTO 2017 iii Dedication To my beloved family iv ACKNOWLEDGMENTS In the name of Allah, the most gracious, most compassionate, most merciful and all the praises and thanks be to Allah that has given me the opportunity and capability to finish my study in KFUPM. I am deeply indebted and most sincere appreciation goes to my advisor, Dr. Assad Al- Thukair, for knowledge, patience, encouragements, and guidance he has shown me over the past few years that I have been with this department, be it scientifically, personally, or academically. I would like to thank my thesis committee members for their support and sharing their knowledge over the years: Dr. Alexis Nzila and Dr. Musa Mohammed Musa. My thanks also are addressed to my wonderful family: my parents, for their endless pray, love and support; my brother and sisters, for keeping my spirit and encouragement during my master journey; and lastly — to my wife for your endless love, support and encouragement has been most influential and inspiring. v TABLE OF CONTENTS ACKNOWLEDGMENTS .............................................................................................. V TABLE OF CONTENTS .............................................................................................. VI LIST OF TABLES ......................................................................................................... X LIST OF FIGURES ...................................................................................................... XI LIST OF ABBREVIATION ...................................................................................... -
Marine Drugs
Mar. Drugs 2015, 13, 4539-4555; doi:10.3390/md13074539 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4 Angela Casillo 1, Ermenegilda Parrilli 1, Sannino Filomena 1,2, Buko Lindner 3, Rosa Lanzetta 1, Michelangelo Parrilli 4, Maria Luisa Tutino 1 and Maria Michela Corsaro 1,* 1 Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, Napoli 80126, Italy; E-Mails: [email protected] (A.C.); [email protected] (E.P.); [email protected] (S.F.); [email protected] (R.L.); [email protected] (M.L.T.) 2 Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, Napoli 80131, Italy 3 Division of Bioanalytical Chemistry, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 10, BorstelD-23845, Germany; E-Mail: [email protected] 4 Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cintia 4, Napoli 80126, Italy; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-081-674149; Fax: +39-081-674393. Academic Editor: Antonio Trincone Received: 22 June 2015 / Accepted: 14 July 2015 /Published: 22 July 2015 Abstract: Psychrophilic microorganisms have successfully colonized all permanently cold environments from the deep sea to mountain and polar regions. The ability of an organism to survive and grow in cryoenviroments depends on a number of adaptive strategies aimed at maintaining vital cellular functions at subzero temperatures, which include the structural modifications of the membrane. -
Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment
RESEARCH ARTICLE Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical Thalassohaline Environment Christophe Leboulanger1*, HeÂlène Agogue 2☯, CeÂcile Bernard3☯, Marc Bouvy1☯, Claire Carre 1³, Maria Cellamare3¤³, Charlotte Duval3³, Eric Fouilland4☯, Patrice Got4☯, Laurent Intertaglia5³, CeÂline Lavergne2³, Emilie Le Floc'h4☯, CeÂcile Roques4³, GeÂrard Sarazin6☯ a1111111111 1 UMR MARBEC, Institut de Recherche pour le DeÂveloppement, Sète-Montpellier, France, 2 UMR LIENSs, Centre National de la Recherche Scientifique, La Rochelle, France, 3 UMR MCAM, MuseÂum National a1111111111 d'Histoire Naturelle, Paris, France, 4 UMR MARBEC, Centre National de la Recherche Scientifique, Sète- a1111111111 Montpellier, France, 5 Observatoire OceÂanologique de Banyuls-sur-Mer, Universite Pierre et Marie Curie, a1111111111 Banyuls-sur-Mer, France, 6 UMR7154 Institut de Physique du Globe de Paris, Universite Paris Diderot, a1111111111 Paris, France ☯ These authors contributed equally to this work. ¤ Current address: Phyto-Quality, 15 rue PeÂtrarque, Paris, France ³ These authors also contributed equally to this work. * [email protected] OPEN ACCESS Citation: Leboulanger C, Agogue H, Bernard C, Bouvy M, Carre C, Cellamare M, et al. (2017) Abstract Microbial Diversity and Cyanobacterial Production in Dziani Dzaha Crater Lake, a Unique Tropical This study describes, for the first time, the water chemistry and microbial diversity in Dziani Thalassohaline Environment. PLoS ONE 12(1): e0168879. doi:10.1371/journal.pone.0168879 Dzaha, a tropical crater lake located on Mayotte Island (Comoros archipelago, Western Indian Ocean). The lake water had a high level of dissolved matter and high alkalinity (10.6± Editor: Jean-FrancËois Humbert, INRA, FRANCE -1 2- 14.5 g L eq. -
Studies on Haloalkaliphilic Gammaproteobacteria from Hypersaline Sambhar Lake, Rajasthan, India
Indian Journal of Geo-Marine Sciences Vol.44(10), October 2015, pp. 1646-1653 Studies on Haloalkaliphilic gammaproteobacteria from hypersaline Sambhar Lake, Rajasthan, India Makarand N. Cherekar & Anupama P. Pathak* School of Life Sciences (DST-FIST & UGC-SAP Sponsored), Swami Ramanand Teerth Marathwada University, Nanded-431606, India. *[E-mail: [email protected]] Received 19 December 2013; revised 04 March 2014 The diversity of haloalkaliphilic gammaproteobacteria from hypersaline Sambhar soda lake, India was analyzed. Four different sampling points were selected within the lake. Nine moderate and extreme isolates were identified using morphological, biochemical and 16S rRNA sequencing method. These isolates were screened for salt, pH and temperature tolerance. In the gammaproteobacteria group, all the selected isolates belonged to one genus Halomonas represented by four different species Halomonas pantelleriensis, Halomonas venusta, Halomonas alkaliphila, and Halomonas sp. All these isolates were capable to grow in 10 -20% NaCl concentrations, 8-12 pH and 20 to 50 oC temperature. These isolates were competent to produce industrially important extracellular hydrolytic enzymes. Most of them were shown to produce cellulase, pectinase and xylanase. [Keywords: Gammaproteobacteria, Halomonas, haloalkaliphilic, Sambhar soda lake, 16S rRNA sequencing] Introduction Sambhar Lake is the largest inland saline lake located Hypersaline soda lakes are considered as extreme in Thar Desert of Rajasthan, India (26o 52’- 27 o 2’ N, environments for microbial life. These lakes are 74 o 53’- 75 o 13’E). It is an elliptical and shallow characterized by high salinity and high alkalinity with lake, with the maximum length of 22.5 km. The width extremely productive environment for extreme of the lake ranges from 3.2 km to 11.2 km. -
Biochemical and Molecular Characterization of Putative Immunoprotective Molecules of the Soft Tick, Ornithodoros Savignyi Audouin (1827)
Biochemical and molecular characterization of putative immunoprotective molecules of the soft tick, Ornithodoros savignyi Audouin (1827) By Po Hsun (Paul) Cheng Submitted in partial fulfillment of the degree Philosophiae Doctor Department of Biochemistry In the Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria November 2010 © University of Pretoria Table of contents Page List of Figures IV List of Tables VI Abbreviations VII Acknowledgements X Summary XII Chapter: 1 Introduction 1 1.1 Problem statement 1 1.2 Ornithodoros savignyi as a model organism for this study 2 1.3 The invertebrate innate immunity 3 1.3.1 Discrimination between self and non-self 4 1.3.2 Cellular immune responses 7 1.3.2.1 Phagocytosis 8 1.3.2.2 Nodulation and encapsulation 9 1.3.2.3 Melanization 10 1.3.3 Humoral immune responses 11 1.3.3.1 AMPs 11 1.3.3.2 Lysozyme 15 1.3.3.3 Proteases and protease inhibitors 18 1.3.4 Coagulation 19 1.3.5 Iron sequestration 19 1.3.6 Oxidative stress 20 1.4 Aims of thesis 21 Chapter 2: Identification of tick proteins recognizing Gram-negative 22 bacteria 2.1 Introduction 22 2.2 Hypothesis 24 2.3 Materials and methods 25 2.3.1 Ticks 25 2.3.2 Reagents 25 2.3.3 E. coli binding proteins in hemolymph plasma from unchallenged 26 ticks 2.3.3.1 Binding assay 26 2.3.3.2 SDS-PAGE analysis of bacteria binding proteins in plasma from 27 unchallenged ticks 2.3.4 E.