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Development and Evaluation of Rrna Targeted in Situ Probes and Phylogenetic Relationships of Freshwater Fungi
Development and evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi vorgelegt von Diplom-Biologin Christiane Baschien aus Berlin Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. sc. techn. Lutz-Günter Fleischer Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: Prof. Dr. rer. nat. Felix Bärlocher Berichter: Dr. habil. Werner Manz Tag der wissenschaftlichen Aussprache: 19.05.2003 Berlin 2003 D83 Table of contents INTRODUCTION ..................................................................................................................................... 1 MATERIAL AND METHODS .................................................................................................................. 8 1. Used organisms ............................................................................................................................. 8 2. Media, culture conditions, maintenance of cultures and harvest procedure.................................. 9 2.1. Culture media........................................................................................................................... 9 2.2. Culture conditions .................................................................................................................. 10 2.3. Maintenance of cultures.........................................................................................................10 -
Aquabacterium Gen. Nov., with Description of Aquabacterium Citratiphilum Sp
International Journal of Systematic Bacteriology (1999), 49, 769-777 Printed in Great Britain Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system Sibylle Kalmbach,’ Werner Manz,’ Jorg Wecke2 and Ulrich Szewzyk’ Author for correspondence : Werner Manz. Tel : + 49 30 3 14 25589. Fax : + 49 30 3 14 7346 1. e-mail : [email protected]. tu-berlin.de 1 Tech nisc he U nive rsit ;it Three bacterial strains isolated from biofilms of the Berlin drinking water Berlin, lnstitut fur system were characterized with respect to their morphological and Tec hn ischen Umweltschutz, Fachgebiet physiological properties and their taxonomic position. Phenotypically, the Okologie der bacteria investigated were motile, Gram-negative rods, oxidase-positive and Mikroorganismen,D-l 0587 catalase-negative, and contained polyalkanoates and polyphosphate as Berlin, Germany storage polymers. They displayed a microaerophilic growth behaviour and 2 Robert Koch-lnstitut, used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfate Nordufer 20, D-13353 Berlin, Germany or ferric iron. The substrates metabolized included a broad range of organic acids but no carbohydrates at all. The three species can be distinguished from each other by their substrate utilization, ability to hydrolyse urea and casein, cellular protein patterns and growth on nutrient-rich media as well as their temperature, pH and NaCl tolerances. Phylogenetic analysis, based on 165 rRNA gene sequence comparison, revealed that the isolates are affiliated to the /I1 -subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44.9 to 51*3O/0. -
Aquabacterium Limnoticum Sp. Nov., Isolated from a Freshwater Spring
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by National Chung Hsing University Institutional Repository International Journal of Systematic and Evolutionary Microbiology (2012), 62, 698–704 DOI 10.1099/ijs.0.030635-0 Aquabacterium limnoticum sp. nov., isolated from a freshwater spring Wen-Ming Chen,1 Nian-Tsz Cho,1 Shwu-Harn Yang,2 A. B. Arun,3 Chiu-Chung Young4 and Shih-Yi Sheu2 Correspondence 1Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine Shih-Yi Sheu University, no. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC [email protected] 2Department of Marine Biotechnology, National Kaohsiung Marine University, no. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC 3Yenepoya Research Center, Yenepoya University, University Rd, Deralakatee, Mangalore, Karnataka State, India 4College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC A Gram-negative, facultatively anaerobic, short-rod-shaped, non-motile and non-spore-forming bacterial strain, designated ABP-4T, was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Growth occurred at 20–40 6C (optimum, 30–37 6C), at pH 7.0–10.0 (optimum, pH 7.0–9.0) and with 0–3 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4T, together with Aquabacterium fontiphilum CS-6T (96.4 % sequence similarity), Aquabacterium commune B8T (96.1 %), Aquabacterium citratiphilum B4T (95.5 %) and Aquabacterium parvum B6T (94.7 %), formed a deep line within the order Burkholderiales. -
Aquabacterium Gen. Nov., with Description of Aquabacterium Citratiphilum Sp
International Journal of Systematic Bacteriology (1999), 49, 769-777 Printed in Great Britain Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system Sibylle Kalmbach,’ Werner Manz,’ Jorg Wecke2 and Ulrich Szewzyk’ Author for correspondence : Werner Manz. Tel : + 49 30 3 14 25589. Fax : + 49 30 3 14 7346 1. e-mail : [email protected]. tu-berlin.de 1 Tech nisc he U nive rsit ;it Three bacterial strains isolated from biofilms of the Berlin drinking water Berlin, lnstitut fur system were characterized with respect to their morphological and Tec hn ischen Umweltschutz, Fachgebiet physiological properties and their taxonomic position. Phenotypically, the Okologie der bacteria investigated were motile, Gram-negative rods, oxidase-positive and Mikroorganismen,D-l 0587 catalase-negative, and contained polyalkanoates and polyphosphate as Berlin, Germany storage polymers. They displayed a microaerophilic growth behaviour and 2 Robert Koch-lnstitut, used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfate Nordufer 20, D-13353 Berlin, Germany or ferric iron. The substrates metabolized included a broad range of organic acids but no carbohydrates at all. The three species can be distinguished from each other by their substrate utilization, ability to hydrolyse urea and casein, cellular protein patterns and growth on nutrient-rich media as well as their temperature, pH and NaCl tolerances. Phylogenetic analysis, based on 165 rRNA gene sequence comparison, revealed that the isolates are affiliated to the /I1 -subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44.9 to 51*3O/0. -
Analysis of the Thermal Stability of Mercuric Reductase from the Hot
American University in Cairo AUC Knowledge Fountain Theses and Dissertations 6-1-2017 Analysis of the thermal stability of mercuric reductase from the hot brine environment of Atlantis II in the Red Sea by site-directed mutagenesis: Structural interpretation of thermolabile and enhanced thermostable mutants Mohamad Maged Galal Follow this and additional works at: https://fount.aucegypt.edu/etds Recommended Citation APA Citation Galal, M. (2017).Analysis of the thermal stability of mercuric reductase from the hot brine environment of Atlantis II in the Red Sea by site-directed mutagenesis: Structural interpretation of thermolabile and enhanced thermostable mutants [Master’s thesis, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/27 MLA Citation Galal, Mohamad Maged. Analysis of the thermal stability of mercuric reductase from the hot brine environment of Atlantis II in the Red Sea by site-directed mutagenesis: Structural interpretation of thermolabile and enhanced thermostable mutants. 2017. American University in Cairo, Master's thesis. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/27 This Dissertation is brought to you for free and open access by AUC Knowledge Fountain. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of AUC Knowledge Fountain. For more information, please contact [email protected]. The American University in Cairo School of Sciences and Engineering Analysis of the thermal stability of mercuric reductase from the hot brine environment of Atlantis II in the Red Sea by site-directed mutagenesis: Structural interpretation of thermolabile and enhanced thermostable mutants By Mohamad Maged A PhD Dissertation submitted in partial fulfillment of the requirements for the degree of PhD in Applied Sciences With specialization in: Biotechnology Under the supervision of Dr. -
Identification and Characterization of Monooxygenase
IDENTIFICATION AND CHARACTERIZATION OF MONOOXYGENASE ENZYMES INVOLVED IN 1,4-DIOXANE DEGRADATION IN PSEUDONOCARDIA SP. STRAIN ENV478, MYCOBACTERIUM SP. STRAIN ENV421, AND NOCARDIA SP. STRAIN ENV425 by HISAKO MASUDA A Dissertation submitted to the Graduate School-New Brunswick Rutgers, The State University of New Jersey And The Graduate school of Biomedical Sciences University of Medicine and Dentistry of New Jersey in partial fulfillment of the requirements for the degree of Doctor of Philosophy Graduate Program in Microbiology and Molecular Genetics written under the direction of Professor Gerben J Zylstra And approved by New Brunswick, New Jersey May, 2009 ABSTRACT OF THE DISSERTATION IDENTIFICATION AND CHARACTERIZATION OF MONOOXYGENASE ENZYMES INVOLVED IN 1,4-DIOXANE DEGRADATION IN PSEUDONOCARDIA SP. STRAIN EVN478, MYCOBACTERIUM SP. STRAIN ENV421, AND NOCARDIA SP. STRAIN ENV425 AND IDENTIFICATION AND CHARACTERIZATION OF AQUABACTERIUM NJENSIS NOV. by HISAKO MASUDA Dissertation director: Professor Gerben J. Zylstra The first part of this dissertation deals with the identification and analysis of oxygenases possibly involved in a biodegradation of a possible human carcinogen, 1, 4- dioxane. The cometabolic oxidations of 1, 4-dioxane in three gram positive bacteria were analyzed. In Mycobacterium sp. ENV421 and Nocardia sp. ENV425, 1, 4-dioxane is oxidized during growth on propane. Three putative propane oxidizing enzymes (alkane monooxygenase, soluble diiron monooxygenase, and cytochrome P450) were identified in both strains. While in strain ENV425 only soluble diiron monooxygenase was expressed after growth on propane, in strain ENV421 all three genes were expressed. Although 1,4-dioxane oxidation activity could not be detected in heterologous host gene expression studies, aliphatic oxidation activity was observed with cytochrome P450 CYP153 from strain ENV421. -
Heterotrophic Plate Counts and Drinking-Water Safety
Heterotrophic Plate Counts and Drinking-water Safety The Significance of HPCs for Water Quality and Human Health Heterotrophic Plate Counts and Drinking-water Safety The Significance of HPCs for Water Quality and Human Health Edited by J. Bartram, J. Cotruvo, M. Exner, C. Fricker, A. Glasmacher Published on behalf of the World Health Organization by IWA Publishing, Alliance House, 12 Caxton Street, London SW1H 0QS, UK Telephone: +44 (0) 20 7654 5500; Fax: +44 (0) 20 7654 5555; Email: [email protected] www.iwapublishing.com First published 2003 World Health Organization 2003 Printed by TJ International (Ltd), Padstow, Cornwall, UK Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the UK Copyright, Designs and Patents Act (1998), no part of this publication may be reproduced, stored or transmitted in any form or by any means, without the prior permission in writing of the publisher, or, in the case of photographic reproduction, in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of licenses issued by the appropriate reproduction rights organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to IWA Publishing at the address printed above. The publisher makes no representation, express or implied, with regard to the accuracy of the information contained in this book and cannot accept any legal responsibility or liability for errors or omissions that may be made. Disclaimer The opinions expressed in this publication are those of the authors and do not necessarily reflect the views or policies of the International Water Association, NSF International, or the World Health Organization. -
Zou Et Al 2020.Pdf
Environmental Factors and Pollution Stresses Select Bacterial Populations in Association With Protists Songbao Zou, Qianqian Zhang, Xiaoli Zhang, Christine Dupuy, Jun Gong To cite this version: Songbao Zou, Qianqian Zhang, Xiaoli Zhang, Christine Dupuy, Jun Gong. Environmental Factors and Pollution Stresses Select Bacterial Populations in Association With Protists. Frontiers in Marine Science, Frontiers Media, 2020, 7, 10.3389/fmars.2020.00659. hal-03097927 HAL Id: hal-03097927 https://hal.archives-ouvertes.fr/hal-03097927 Submitted on 5 Jan 2021 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. fmars-07-00659 August 7, 2020 Time: 15:29 # 1 ORIGINAL RESEARCH published: 07 August 2020 doi: 10.3389/fmars.2020.00659 Environmental Factors and Pollution Stresses Select Bacterial Populations in Association With Protists Songbao Zou1,2,3, Qianqian Zhang1, Xiaoli Zhang1, Christine Dupuy4 and Jun Gong3,5* 1 Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China, 2 University of Chinese Academy of Sciences, Beijing, China, 3 School of Marine Sciences, Sun Yat-sen University, Zhuhai, China, 4 Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS, University of La Rochelle, La Rochelle, France, 5 Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China Digestion-resistant bacteria (DRB) refer to the ecological bacterial group that can be ingested, but not digested by protistan grazers, thus forming a specific type of bacteria-protist association. -
Bacterial Community Colonization on Tire Microplastics in Typical Urban Water Environments and Associated Impacting Factors
Journal Pre-proof Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors Liyuan Wang, Zhuanxi Luo, Zhuo Zhen, Yu Yan, Changzhou Yan, Xiaofei Ma, Lang Sun, Mei Wang, Xinyi Zhou, Anyi Hu PII: S0269-7491(20)30246-3 DOI: https://doi.org/10.1016/j.envpol.2020.114922 Reference: ENPO 114922 To appear in: Environmental Pollution Received Date: 11 January 2020 Revised Date: 17 May 2020 Accepted Date: 30 May 2020 Please cite this article as: Wang, L., Luo, Z., Zhen, Z., Yan, Y., Yan, C., Ma, X., Sun, L., Wang, M., Zhou, X., Hu, A., Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors, Environmental Pollution (2020), doi: https:// doi.org/10.1016/j.envpol.2020.114922. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2020 Published by Elsevier Ltd. 1 BBBacterialBacterial community colonization on tire microplastics in 2 typical urban water environments and associated 3 impacting factors ∗ 4 Liyuan -
Microbiota Assembly and Dissolved Organic Matter Diversity in Natural Mineral Waters Celine C
Lesaulnier et al. Microbiome (2017) 5:126 DOI 10.1186/s40168-017-0344-9 RESEARCH Open Access Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters Celine C. Lesaulnier1†, Craig W. Herbold1†, Claus Pelikan1, David Berry1, Cédric Gérard4, Xavier Le Coz4, Sophie Gagnot4, Jutta Niggemann3, Thorsten Dittmar3, Gabriel A. Singer2† and Alexander Loy1* Abstract Background: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown. Results: We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM. Conclusions: The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules. -
Correlation of Seasonal Nitrification Failure and Ammonia-Oxidizing Community Dynamics in a Wastewater Treatment Plant Treating Water from a Saline Thermal Spa
Ann Microbiol (2014) 64:1671–1682 DOI 10.1007/s13213-014-0811-5 ORIGINAL ARTICLE Correlation of seasonal nitrification failure and ammonia-oxidizing community dynamics in a wastewater treatment plant treating water from a saline thermal spa Luciano Beneduce & Giuseppe Spano & Francesco Lamacchia & Micol Bellucci & Francesco Consiglio & Ian M. Head Received: 21 August 2013 /Accepted: 9 January 2014 /Published online: 24 January 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract In this work we evaluated the effect of a perturba- sampling period. This study reports a clear association of tion on nitrification performance in a wastewater treatment microbial community dynamics (strongly correlated to salin- plant (WWTP) treating urban and saline thermal bath waste- ity, temperature, and dissolved oxygen) to nitrification perfor- water, which regularly occurred during summer months. We mance. Particularly, ammonia-oxidizing bacteria are severely wanted to find out if this related to changes in the ammonia affected by drastic changes in operational conditions, with oxidizing communities. The bacterial and ammonia-oxidizing direct consequences on WWTP performance. bacterial (AOB) community from three different basins of the WWTP were evaluated using PCR-DGGE and cloning and Keywords Activated sludge . DGGE (denaturing gradient gel sequencing of 16S rRNA gene fragments, over a six month electrophoresis) . Diversity . Nitrification . AOB . Wastewater survey. Both eubacterial and AOB communities underwent treatment continuous change over time, with a particularly prominent shift between the third and fourth month of monitoring for eubacteria and the fourth month and fifth month for AOB. At Introduction the same time, reduction of nitrification performance was observed in the WWTP. -
Letter to the Editor Bacterial Communities Associated with An
646 Biomed Environ Sci, 2014; 27(8): 646-650 Letter to the Editor Bacterial Communities Associated with An Occurrence of Colored Water in An Urban Drinking Water Distribution System* WU Hui Ting1,2,△, MI Zi Long1,2,△, ZHANG Jing Xu3, CHEN Chao1,2, and XIE Shu Guang3,# This study aimed to investigate bacterial majority of urban areas reported the occurrence of community in an urban drinking water distribution colored water, but the water quality in some areas system (DWDS) during an occurrence of colored was still normal, without perceptible color. Water water. Variation in the bacterial community samples were collected from three colored water diversity and structure was observed among the points A, B and C, and a normal point D (as a different waters, with the predominance of reference point). All water samples were Proteobacteria. While Verrucomicrobia was also a immediately processed after collection. The major phylum group in colored water. Limnobacter physicochemical features of the four water samples was the major genus group in colored water, but are shown in Table S1. Undibacterium predominated in normal tap water. For analysis of aquatic bacterial community, The coexistence of Limnobacter as well as water samples (5 L) were filtered through 0.22-µm Sediminibacterium and Aquabacterium might pore-size membranes (diameter 50 mm; Millipore, contribute to the formation of colored water. USA). The membrane filters stored at -20 °C for The drinking water distribution system (DWDS) further molecular analysis. DNA samples were is mainly composed of iron and steel pipes in many extracted using the E.Z.N.A.® Water DNA kit (Omega, countries that are subject to corrosion during USA) according to the manufacturer’s protocol.