Spatial Distribution of Prokaryotic Symbionts and Ammoxidation
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A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium Smegmatis Is Involved in De Novo Cysteine Biosynthesis
University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 5-2020 A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis Saroj Kumar Mahato University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Molecular Biology Commons, and the Pathogenic Microbiology Commons Citation Mahato, S. K. (2020). A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis. Theses and Dissertations Retrieved from https://scholarworks.uark.edu/etd/3639 This Thesis is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. A Putative Cystathionine Beta-Synthase Homolog of Mycolicibacterium smegmatis is Involved in de novo Cysteine Biosynthesis A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Cell and Molecular Biology by Saroj Kumar Mahato Purbanchal University Bachelor of Science in Biotechnology, 2016 May 2020 University of Arkansas This thesis is approved for recommendation to the Graduate Council. ___________________________________ Young Min Kwon, Ph.D. Thesis Director ___________________________________ ___________________________________ Suresh Thallapuranam, Ph.D. Inés Pinto, Ph.D. Committee Member Committee Member ABSTRACT Mycobacteria include serious pathogens of humans and animals. Mycolicibacterium smegmatis is a non-pathogenic model that is widely used to study core mycobacterial metabolism. This thesis explores mycobacterial pathways of cysteine biosynthesis by generating and study of genetic mutants of M. smegmatis. Published in vitro biochemical studies had revealed three independent routes to cysteine synthesis in mycobacteria involving separate homologs of cysteine synthase, namely CysK1, CysK2, and CysM. -
Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Bioactive Compounds from the Marine Sponge Geodia Barretti
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Pharmacy 32 Bioactive Compounds from the Marine Sponge Geodia barretti Characterization, Antifouling Activity and Molecular Targets MARTIN SJÖGREN ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6192 UPPSALA ISBN 91-554-6534-X 2006 urn:nbn:se:uu:diva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eodia barretti , s y m ' i " Balanus improvius a ' 56C! ! %& ' ! ' ( )*+' ' ,-*)./0 ' # E ./0' #$ 4..5 $6$%# 4.5 %676$768 -
Functional Equivalence and Evolutionary Convergence In
Functional equivalence and evolutionary convergence PNAS PLUS in complex communities of microbial sponge symbionts Lu Fana,b, David Reynoldsa,b, Michael Liua,b, Manuel Starkc,d, Staffan Kjelleberga,b,e, Nicole S. Websterf, and Torsten Thomasa,b,1 aSchool of Biotechnology and Biomolecular Sciences and bCentre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia; cInstitute of Molecular Life Sciences and dSwiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland; eSingapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Republic of Singapore; and fAustralian Institute of Marine Science, Townsville, Queensland 4810, Australia Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved May 21, 2012 (received for review February 24, 2012) Microorganisms often form symbiotic relationships with eukar- ties (11, 12). Symbionts also can be transmitted vertically through yotes, and the complexity of these relationships can range from reproductive cells and larvae, as has been demonstrated in those with one single dominant symbiont to associations with sponges (13, 14), insects (15), ascidians (16), bivalves (17), and hundreds of symbiont species. Microbial symbionts occupying various other animals (18). Vertical transmission generally leads equivalent niches in different eukaryotic hosts may share func- to microbial communities with limited variation in taxonomy and tional aspects, and convergent genome evolution has been function among host individuals. reported for simple symbiont systems in insects. However, for Niches with similar selections may exist in phylogenetically complex symbiont communities, it is largely unknown how prev- divergent hosts that lead comparable lifestyles or have similar alent functional equivalence is and whether equivalent functions physiological properties. -
Comparing Deep-Sea Sponges of the Species Geodia Barretti from Different Locations in the North Atlantic
Comparing deep-sea sponges of the species Geodia barretti from different locations in the North Atlantic Isabel Ordaz Németh The study of genetic and geographic structures of populations for poorly studied species is not exactly straightforward. It is difficult to accurately compare populations of a species from which no genetic data is available. So, is there a way of comparing populations of such as species? There is one possibility, which is by using genetic markers called “Exon-Primed Intron- Crossing” (EPIC) markers. These markers, which are first designed for well-studied species, find a specific piece of DNA that all individuals of a species have. So, by using the markers we can, for example, take the same DNA fragment from several individuals that come from different locations. Then we translate the DNA fragments of these individuals and look at how different they are. This can give us a lot of information about the relationships within and between the populations of a species, as well as its history. Since a lot of genetic information is conserved across different species, we can test these markers on a species that we barely know, and the probability of finding a corresponding DNA fragment can still be quite high. EPIC markers could be very useful for different studies but they haven’t been extensively used since they are relatively new. In this project, the markers were tested on samples of the deep-sea sponge Geodia barretti. The sponges that were used came from different locations; from the Mediterranean Sea, to the coast of Norway, and all the way to the other side of the Atlantic, by the Eastern coast of Canada. -
Background Document for Deep-Sea Sponge Aggregations 2010
Background Document for Deep-sea sponge aggregations Biodiversity Series 2010 OSPAR Convention Convention OSPAR The Convention for the Protection of the La Convention pour la protection du milieu Marine Environment of the North-East Atlantic marin de l'Atlantique du Nord-Est, dite (the “OSPAR Convention”) was opened for Convention OSPAR, a été ouverte à la signature at the Ministerial Meeting of the signature à la réunion ministérielle des former Oslo and Paris Commissions in Paris anciennes Commissions d'Oslo et de Paris, on 22 September 1992. The Convention à Paris le 22 septembre 1992. La Convention entered into force on 25 March 1998. It has est entrée en vigueur le 25 mars 1998. been ratified by Belgium, Denmark, Finland, La Convention a été ratifiée par l'Allemagne, France, Germany, Iceland, Ireland, la Belgique, le Danemark, la Finlande, Luxembourg, Netherlands, Norway, Portugal, la France, l’Irlande, l’Islande, le Luxembourg, Sweden, Switzerland and the United Kingdom la Norvège, les Pays-Bas, le Portugal, and approved by the European Community le Royaume-Uni de Grande Bretagne and Spain. et d’Irlande du Nord, la Suède et la Suisse et approuvée par la Communauté européenne et l’Espagne. Acknowledgement This document has been prepared by Dr Sabine Christiansen for WWF as lead party. Rob van Soest provided contact with the surprisingly large sponge specialist group, of which Joana Xavier (Univ. Amsterdam) has engaged most in commenting on the draft text and providing literature. Rob van Soest, Ole Tendal, Marc Lavaleye, Dörte Janussen, Konstantin Tabachnik, Julian Gutt contributed with comments and updates of their research. -
Mycobacterium Gilvum Spyr1
Standards in Genomic Sciences (2011) 5:144-153 DOI:10.4056/sigs.2265047 Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1 Aristeidis Kallimanis1, Eugenia Karabika1, Kostantinos Mavromatis2, Alla Lapidus2, Kurt M. LaButti2, Konstantinos Liolios2, Natalia Ivanova2, Lynne Goodwin2,3, Tanja Woyke2, Athana- sios D. Velentzas4, Angelos Perisynakis1, Christos C. Ouzounis5§, Nikos C. Kyrpides2, Anna I. Koukkou1*, and Constantin Drainas1† 1 Sector of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, 15701, Athens, Greece 5 Centre for Bioinformatics, Department of Informatics, School of Natural & Mathematical Sciences, King's College London (KCL), London WC2R 2LS, UK § Present address: Computational Genomics Unit, Institute of Agrobiotechnology, Center for Research & Technology Hellas (CERTH), GR-57001 Thessaloniki, Greece & Donnelly Cen- tre for Cellular & Biomolecular Research, University of Toronto, 160 College Street, To- ronto, Ontario M5S 3E1, Canada *Corresponding author: Anna I. Koukkou, email: [email protected] † In memory of professor Constantin Drainas who lost his life in a car accident on July 5th, 2011. Mycobacterium sp.Spyr1 is a newly isolated strain that occurs in a creosote contaminated site in Greece. It was isolated by an enrichment method using pyrene as sole carbon and energy source and is capable of degrading a wide range of PAH substrates including pyrene, fluoran- thene, fluorene, anthracene and acenapthene. Here we describe the genomic features of this organism, together with the complete sequence and annotation. -
The Bacterial Communities of Sand-Like Surface Soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang
The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Yang Wang To cite this version: Yang Wang. The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA). Agricultural sciences. Université Paris-Saclay, 2015. English. NNT : 2015SACLS120. tel-01261518 HAL Id: tel-01261518 https://tel.archives-ouvertes.fr/tel-01261518 Submitted on 25 Jan 2016 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. NNT : 2015SACLS120 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N°577 Structure et Dynamique des Systèmes Vivants Spécialité de doctorat : Sciences de la Vie et de la Santé Par Mme Yang WANG The bacterial communities of sand-like surface soils of the San Rafael Swell (Utah, USA) and the Desert of Maine (USA) Thèse présentée et soutenue à Orsay, le 23 Novembre 2015 Composition du Jury : Mme. Marie-Claire Lett , Professeure, Université Strasbourg, Rapporteur Mme. Corinne Cassier-Chauvat , Directeur de Recherche, CEA, Rapporteur M. Armel Guyonvarch, Professeur, Université Paris-Sud, Président du Jury M. -
Sponge Grounds As Key Marine Habitats: a Synthetic Review of Types, Structure, Functional Roles, and Conservation Concerns
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/300316780 Sponge Grounds as Key Marine Habitats: A Synthetic Review of Types, Structure, Functional Roles, and Conservation Concerns Chapter · April 2016 DOI: 10.1007/978-3-319-17001-5_24-1 CITATIONS READS 10 1,765 17 authors, including: Manuel Maldonado Ricardo Aguilar Spanish National Research Council Oceana 125 PUBLICATIONS 3,487 CITATIONS 57 PUBLICATIONS 354 CITATIONS SEE PROFILE SEE PROFILE Raymond John Bannister James Bell Institute of Marine Research in Norway Victoria University of Wellington 32 PUBLICATIONS 418 CITATIONS 202 PUBLICATIONS 3,091 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Atlantic sponges View project Transgenerational acclimation of sponges in a changing environment View project All content following this page was uploaded by Ellen L. Kenchington on 24 April 2018. The user has requested enhancement of the downloaded file. Sponge Grounds as Key Marine Habitats: A Synthetic Review of Types, Structure, Functional Roles, and Conservation Concerns Manuel Maldonado, Ricardo Aguilar, Raymond J. Bannister, James J. Bell, Kim W. Conway, Paul K. Dayton, Cristina Díaz, Julian Gutt, Michelle Kelly, Ellen L. R. Kenchington, Sally P. Leys, Shirley A. Pomponi, Hans Tore Rapp, Klaus Rutzler,€ Ole S. Tendal, Jean Vacelet, and Craig M. Young Contents 1 Introduction .................................................................................. 3 -
Arcanobacterium Haemolyticum Type Strain (11018)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). Permalink https://escholarship.org/uc/item/03f632gf Journal Standards in genomic sciences, 3(2) ISSN 1944-3277 Authors Yasawong, Montri Teshima, Hazuki Lapidus, Alla et al. Publication Date 2010-09-28 DOI 10.4056/sigs.1123072 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:126-135 DOI:10.4056/sigs.1123072 Complete genome sequence of Arcanobacterium T haemolyticum type strain (11018 ) Montri Yasawong1, Hazuki Teshima2,3, Alla Lapidus2, Matt Nolan2, Susan Lucas2, Tijana Glavina Del Rio2, Hope Tice2, Jan-Fang Cheng2, David Bruce2,3, Chris Detter2,3, Roxanne Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde1, Johannes Sikorski6, Rüdiger Pukall6, Markus Göker6, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2, Nikos C. Kyrpides2, and Hans-Peter Klenk6* 1 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: obligate parasite, human pathogen, pharyngeal lesions, skin lesions, facultative anaerobe, Actinomycetaceae, Actinobacteria, GEBA Arcanobacterium haemolyticum (ex MacLean et al. -
Biodegradation Treatment of Petrochemical Wastewaters
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA VEGETAL Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre Dissertação Mestrado em Microbiologia Aplicada Orientadores Doutora Sandra Sanches Professora Doutora Lélia Chambel 2015 Biodegradation treatment of petrochemical wastewaters Catarina Isabel Nunes Alexandre 2015 This thesis was fully performed at the Institute of Experimental and Technologic Biology (IBET) of Instituto de Tecnologia Química e Bioquímica (ITQB) under the direct supervision of Drª Sandra Sanches in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Prof. Drª Lélia Chambel was the internal designated supervisor in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon. Agradecimentos Gostaria de agradecer a todas as pessoas que estiveram directamente ou indirectamente envolvidas na execução da minha tese de mestrado, pois sem eles a sua realização não teria sido possível. Queria começar por agradecer à Doutora Sandra Sanches, que se demonstrou sempre disponível para esclarecer dúvidas quando precisei, e que fez questão de me ensinar de forma rigorosa e exigente. À Doutora Maria Teresa Crespo, que assim que lhe pedi para me orientar me disse que sim imediatamente, fez questão de me treinar em vários contextos e sempre estimulou o meu envolvimento nas rotinas do laboratório. À Professora Doutora Lélia Chambel, que sempre me esclareceu dúvidas sobre processos burocráticos, me deu conselhos quando eu mais precisei e que me apoiou durante toda a minha tese. Queria também agradecer à Doutora Dulce Brito, que sempre se mostrou disponível para ajudar quando a nossa equipa mais precisava dela, e sempre me ajudou a realizar as tarefas mais básicas do meu trabalho até eu ter ganho a minha autonomia no laboratório. -
Shifts in Archaeaplankton Community Structure Along Ecological Gradients of Pearl Estuary Jiwen Liu1, Shaolan Yu1, Meixun Zhao2, Biyan He3,4 & Xiao-Hua Zhang1
RESEARCH ARTICLE Shifts in archaeaplankton community structure along ecological gradients of Pearl Estuary Jiwen Liu1, Shaolan Yu1, Meixun Zhao2, Biyan He3,4 & Xiao-Hua Zhang1 1College of Marine Life Sciences, Ocean University of China, Qingdao, China; 2Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China; 3State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China; and 4School of Bioengineering, Jimei University, Xiamen, China Downloaded from https://academic.oup.com/femsec/article/90/2/424/2680468 by guest on 01 October 2021 Correspondence: Xiao-Hua Zhang, College Abstract of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, The significance of archaea in regulating biogeochemical processes has led to China. Tel./fax: +86 532 82032767; an interest in their community compositions. Using 454 pyrosequencing, the e-mail: [email protected] present study examined the archaeal communities along a subtropical estuary, Pearl Estuary, China. Marine Group I Thaumarchaeota (MG-I) were predomi- Received 18 April 2014; revised 29 July nant in freshwater sites and one novel subgroup of MG-I, that is MG-Im, was 2014; accepted 31 July 2014. Final version proposed. In addition, the previously defined MG-Ia II was grouped into two published online 28 August 2014. clusters (MG-Ia II-1, II-2). MG-Ia II-1 and MG-Ik II were both freshwater- a k DOI: 10.1111/1574-6941.12404 specific, with MG-I II-1 being prevalent in the oxic water and MG-I II in the hypoxic water. Salinity, dissolved oxygen, nutrients and pH were the most Editor: Gary King important determinants that shaped the differential distribution of MG-I sub- groups along Pearl Estuary.