Qualitative and Quantitative Assessment of the “Dangerous
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Actinobacterial Diversity of the Ethiopian Rift Valley Lakes
ACTINOBACTERIAL DIVERSITY OF THE ETHIOPIAN RIFT VALLEY LAKES By Gerda Du Plessis Submitted in partial fulfillment of the requirements for the degree of Magister Scientiae (M.Sc.) in the Department of Biotechnology, University of the Western Cape Supervisor: Prof. D.A. Cowan Co-Supervisor: Dr. I.M. Tuffin November 2011 DECLARATION I declare that „The Actinobacterial diversity of the Ethiopian Rift Valley Lakes is my own work, that it has not been submitted for any degree or examination in any other university, and that all the sources I have used or quoted have been indicated and acknowledged by complete references. ------------------------------------------------- Gerda Du Plessis ii ABSTRACT The class Actinobacteria consists of a heterogeneous group of filamentous, Gram-positive bacteria that colonise most terrestrial and aquatic environments. The industrial and biotechnological importance of the secondary metabolites produced by members of this class has propelled it into the forefront of metagenomic studies. The Ethiopian Rift Valley lakes are characterized by several physical extremes, making it a polyextremophilic environment and a possible untapped source of novel actinobacterial species. The aims of the current study were to identify and compare the eubacterial diversity between three geographically divided soda lakes within the ERV focusing on the actinobacterial subpopulation. This was done by means of a culture-dependent (classical culturing) and culture-independent (DGGE and ARDRA) approach. The results indicate that the eubacterial 16S rRNA gene libraries were similar in composition with a predominance of α-Proteobacteria and Firmicutes in all three lakes. Conversely, the actinobacterial 16S rRNA gene libraries were significantly different and could be used to distinguish between sites. -
Correction: Genomic Comparison of 93 Bacillus Phages Reveals 12 Clusters
Grose et al. BMC Genomics 2014, 15:1184 http://www.biomedcentral.com/1471-2164/15/1184 CORRECTION Open Access Correction: genomic comparison of 93 Bacillus phages reveals 12 clusters, 14 singletons and remarkable diversity Julianne H Grose*, Garrett L Jensen, Sandra H Burnett and Donald P Breakwell Abstract Background: The Bacillus genus of Firmicutes bacteria is ubiquitous in nature and includes one of the best characterized model organisms, B. subtilis, as well as medically significant human pathogens, the most notorious being B. anthracis and B. cereus. As the most abundant living entities on the planet, bacteriophages are known to heavily influence the ecology and evolution of their hosts, including providing virulence factors. Thus, the identification and analysis of Bacillus phages is critical to understanding the evolution of Bacillus species, including pathogenic strains. Results: Whole genome nucleotide and proteome comparison of the 83 extant, fully sequenced Bacillus phages revealed 10 distinct clusters, 24 subclusters and 15 singleton phages. Host analysis of these clusters supports host boundaries at the subcluster level and suggests phages as vectors for genetic transfer within the Bacillus cereus group, with B. anthracis as a distant member. Analysis of the proteins conserved among these phages reveals enormous diversity and the uncharacterized nature of these phages, with a total of 4,442 protein families (phams) of which only 894 (20%) had a predicted function. In addition, 2,583 (58%) of phams were orphams (phams containing a single member). The most populated phams were those encoding proteins involved in DNA metabolism, virion structure and assembly, cell lysis, or host function. -
Chorioméningite Lymphocytaire, Tuberculose, Échinococcose…
LES ZOONOSES INFECTIEUSES Juin 2021 Ce document vous est offert par Boehringer Ingelheim Ce fascicule fait partie de l’ensemble des documents polycopiés rédigés de manière concertée par des enseignants de maladies contagieuses des quatre Ecoles nationales vétérinaires françaises, à l’usage des étudiants vétérinaires. Sa rédaction et sa mise à jour régulière ont été sous la responsabilité de B. Toma jusqu’en 2006, avec la contribution, pour les mises à jour, de : G. André-Fontaine, M. Artois, J.C. Augustin, S. Bastian, J.J. Bénet, O. Cerf, B. Dufour, M. Eloit, N. Haddad, A. Lacheretz, D.P. Picavet, M. Prave La mise à jour est réalisée depuis 2007 par N. Haddad La citation bibliographique de ce fascicule doit être faite de la manière suivante : Haddad N. et al. Les zoonoses infectieuses, Polycopié des Unités de maladies réglementées des Ecoles vétérinaires françaises, Boehringer Ingelheim (Lyon), juin 2021, 217 p. Nous remercions Boehringer Ingelheim qui, depuis de nombreuses années, finance et assure la réalisation de ce polycopié. * 1 2 OBJECTIFS D’APPRENTISSAGE Rang A (libellé souligné) et rang B A l’issue de cet enseignement, les étudiants devront être capables : • de répondre à des questions posées par une personne (propriétaire d'animaux, médecin...) relatives à la nature des principales maladies bactériennes et virales transmissibles à l'Homme lors de morsure par un carnivore . • de répondre à des questions posées par une personne (propriétaire d'animaux, médecin...) relatives à l'évolution de la maladie chez l'Homme, les modalités de la transmission et de la prévention des principales maladies bactériennes et virales transmissibles à l'Homme à partir des carnivores domestiques et les grandes lignes de leur prophylaxie. -
Investigation of Bacteria Associated with Australian Wine Grapes Using Cultural and Molecular Methods
Investigation of bacteria associated with Australian wine grapes using cultural and molecular methods Sung Sook Bae A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy University of New South Wales Food Science and Technology School of Chemical Engineering and Industrial Chemistry Sydney, Australia 2005 i DECLARATION I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of materials which have been accepted for the award of any other degree or diploma at UNSW or any other education institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project’s design and conception or in style, presentation and linguistic expression is acknowledged. Sung Sook Bae ii ACKNOWLEDGEMENTS I owe a tremendous debt of gratitude to numerous individuals who have contributed to the completion of this work, and I wish to thank them for their contribution. Firstly and foremost, my sincere appreciation goes to my supervisor, Professor Graham Fleet. He has given me his time, expertise, constant guidance and inspiration throughout my study. I also would like to thank my co-supervisor, Dr. Gillian Heard for her moral support and words of encouragement. I am very grateful to the Australian Grape and Wine Research Development and Corporation (GWRDC) for providing funds for this research. -
A Moderately Boron-Tolerant Candidatus Novel Soil Bacterium Lysinibacillus Pakistanensis Sp
Pak. J. Bot., 45(SI): 41-50, January 2013. A MODERATELY BORON-TOLERANT CANDIDATUS NOVEL SOIL BACTERIUM LYSINIBACILLUS PAKISTANENSIS SP. NOV. CAND., ISOLATED FROM SOYBEAN (GLYCINE MAX L.) RHIZOSPHERE RIFAT HAYAT1,2,3*, IFTIKHAR AHMED2*, JAYOUNG PAEK4, MUHAMMAD EHSAN1, 2, MUHAMMAD IQBAL2 AND YOUNG H. CHANG4* 1Department of Soil Science & SWC, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan 2Plant Biotechnology Program, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad-45500, Pakistan 3Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan 4Korean Collection of Type Cultures, Biological Resource Center, KRIBB, 52 Oeundong, Daejeon 305-806, Republic of Korea *Correspondence E-mail: [email protected]; [email protected]; [email protected] Abstract A Gram-positive, motile, rod-shaped, endospore-forming and moderately boron (B) tolerant novel candidatus strain, designated as NCCP-54T, was isolated from rhizospheric soil of soybean (Glycine max L.) sampled from the experimental area of Research Farm, PMAS Arid Agriculture University, Rawalpindi, Pakistan. To delineate its taxonomic position, the strain was subject to polyphasic characterization. Cells of the strain NCCP-54T can grow at 10-45○C (optimum at 28○C) at pH ranges of 6.5-9.0 (optimum at pH 7.0) and in 0-6% NaCl (w/v) in tryptic soya agar medium. It can also tolerate 150 mM boric acid in agar medium; however, optimum growth occurs in the absence of boric acid. Based on 16S rRNA gene sequence analysis, strain NCCP-54T showed highest similarity to Lysinibacillus xylanilyticus KCTC13423T (99.1%), Lysinibacillus fusiformis KCTC3454T (98.5%), Lysinibacillus boronitolerans KCTC13709T (98.4%), Lysinibacillus parviboronicapiens KCTC13154T (97.8%), and Lysinibacillus sphaericus KCTC3346T (97.5%) and less than 97% with other closely related taxa. -
Bacillus Crassostreae Sp. Nov., Isolated from an Oyster (Crassostrea Hongkongensis)
International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1561–1566 DOI 10.1099/ijs.0.000139 Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis) Jin-Hua Chen,1,2 Xiang-Rong Tian,2 Ying Ruan,1 Ling-Ling Yang,3 Ze-Qiang He,2 Shu-Kun Tang,3 Wen-Jun Li,3 Huazhong Shi4 and Yi-Guang Chen2 Correspondence 1Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Yi-Guang Chen Hunan Agricultural University, 410128 Changsha, PR China [email protected] 2College of Biology and Environmental Sciences, Jishou University, 416000 Jishou, PR China 3The Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, 650091 Kunming, PR China 4Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T was able to grow with 0–13 % (w/v) NaCl (optimum 2–5 %), at pH 5.5–10.0 (optimum pH 7.5) and at 5–50 6C (optimum 30–35 6C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0,C16 : 0 and C16 : 1v11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. -
Heterotrophic Denitrification by Gram-Positive Bacteria: Bacillus Cereus and Bacillus Tequilensis
International Journal of Scientific and Research Publications, Volume 4, Issue 4, April 2014 1 ISSN 2250-3153 Heterotrophic denitrification by Gram-positive bacteria: Bacillus cereus and Bacillus tequilensis Moukhlissi Saïd*, Aboussabiq Fatima Ezzahra*, Amine Jamal*, Rihani Mohammed* and Assobhei Omar* * Laboratory of Marine Biotechnology and Environment, Faculty of Science of El Jadida, P.O. Box 20, El Jadida 24000, Morocco. Abstract- Two bacteria were isolated from anoxic denitrifying notoriously overlooked in community analysis of denitrifiers in reactor for treatment of domestic wastewater. The analysis of the the environment because they are not targeted by the available 16S rDNA gene sequences showed that the isolated strains were PCR primers designed for denitrification genes (Throbäck et al., affiliated with Bacillus cereus and Bacillus tequilensis. 2004). Verbaendert et al. (2011) have studied the denitrification Denitrification was compared between Bacillus cereus and of a large collection of Bacillus strains and suggested that Bacillus tequilensis in this study. Two bacilli were able to denitrification occurred in nearly half of the analysed strains. denitrify and Bacillus cereus was more efficient than Bacillus More recently, a variety of bacilli were tested for gas production tequilensis. Bacillus cereus reduced 80% of high amount of under denitrifying conditions and found to be complete nitrate; however, Bacillus tequilensis could reduce 37.4% of denitrifiers (Jones et al., 2011). Genome sequencing has revealed nitrate. These heterotrophic bacteria are able to eliminate organic the potential for partial denitrification in some Bacillus species. matter with the same trend reducing 74.5% for Bacillus For example, qNor is present in Bacillus tusciae strain DSM2912 tequilensis and 70.2% for Bacillus cereus. -
Diapositiva 1
Simultaneous outbreak of Dengue and Chikungunya in Al Hodayda, Yemen (epidemiological and phylogenetic findings) Giovanni Rezza1, Gamal El-Sawaf2, Giovanni Faggioni3, Fenicia Vescio1, Ranya Al Ameri4, Riccardo De Santis3, Ghada Helaly2, Alice Pomponi3, Alessandra Lo Presti1, Dalia Metwally2, Massimo Fantini5, FV, Hussein Qadi4, Massimo Ciccozzi1, Florigio Lista3 1Department of lnfectious, Parasitic and lmmunomediated Diseases, Istituto Superiore di Sanità, Roma, Italy; 2 Medical Research lnstitute- Alexandria University, Egypt; 3Histology and Molecular Biology Section, Army Medical an d Veterinary Research Center, Roma, ltaly; 4 University of Sana’a, Republic of Yemen; 5Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Roma, ltaly * * Background Fig.1 * * Yemen, which is located in the southwestern end of the Arabian Peninsula, is one of the * countries most affected by recurrent epidemics of dengue. * I We conducted a study on individuals hospitalized with dengue-like syndrome in Al Hodayda, with the aim of identifying viral agents responsible of febrile illness (i.e., dengue [DENV], chikungunya [CHIKV], Rift Valley [RVFV] and hemorrhagic fever virus Alkhurma). * * * Methods * The study site was represented by five hospital centers located in Al-Hodayda, United Republic * of Yemen. Patients were recruited in 2011 and 2012. Serum samples were analysed by ELISA * for the presence of IgM antibody against DENV and CHIKV by using commercial assays. Nucleic * acids were extracted by automated method and analyzed by using specific PCR for the Fig. 2 presence of sequences of DENV, RVF virus, Alkhurma virus and CHIKV. To confirm the results, 15 DENV positive sera underwent specific NS1 gene amplification and sequencing reaction. Similarly, CHIKV positive sera were thoroughly investigated by amplification and sequencing Conclusions the gene encoding the E1 protein. -
Generic Amplification and Next Generation Sequencing Reveal
Dinçer et al. Parasites & Vectors (2017) 10:335 DOI 10.1186/s13071-017-2279-1 RESEARCH Open Access Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey Ender Dinçer1†, Annika Brinkmann2†, Olcay Hekimoğlu3, Sabri Hacıoğlu4, Katalin Földes4, Zeynep Karapınar5, Pelin Fatoş Polat6, Bekir Oğuz5, Özlem Orunç Kılınç7, Peter Hagedorn2, Nurdan Özer3, Aykut Özkul4, Andreas Nitsche2 and Koray Ergünay2,8* Abstract Background: Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens. Results: A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. -
Identification of Salt Accumulating Organisms from Winery Wastewater
Identification of salt accumulating organisms from winery wastewater FINAL REPORT to GRAPE AND WINE RESEARCH & DEVELOPMENT CORPORATION Project Number: UA08/01 Principal Investigator: Paul Grbin Research Organisation: University of Adelaide Date: 22/09/10 1 Identification of salt accumulating organisms from winery wastewater Dr Paul R Grbin Dr Kathryn L Eales Dr Frank Schmid Assoc. Prof. Vladimir Jiranek The University of Adelaide School of Agriculture, Food and Wine PMB 1, Glen Osmond, SA 5064 AUSTRALIA Date: 15 January 2010 Publisher: University of Adelaide Disclaimer: The advice presented in this document is intended as a source of information only. The University of Adelaide (UA) accept no responsibility for the results of any actions taken on the basis of the information contained within this publication, nor for the accuracy, currency or completeness of any material reported and therefore disclaim all liability for any error, loss or other consequence which may arise from relying on information in this publication. 2 Table of contents Abstract 3 Executive Summary 4 Background 5 Project Aims and Performance Targets 6 Methods 7 Results and Discussion 11 Outcomes and Conclusions 23 Recommendations 24 Appendix 1: Communication Appendix 2: Intellectual Property Appendix 3: References Appendix 4: Staff Appendix 5: Acknowledgements Appendix 6: Budget Reconciliation 3 Abbreviations: COD: Chemical oxygen demand Ec: Electrical conductivity FACS: Fluorescence activated cell sorting HEPES: 4‐(2‐hydroxyethyl)‐1‐piperazineethanesulfonic acid OD: Optical density PBFI: Potassium benzofuran isophthalate PI: Propidium iodide SAR: Sodium adsorption ratio WWW: Winery wastewater Abstract: In an attempt to find microorganisms that would remove salts from biological winery wastewater (WWW) treatment plants, 8 halophiles were purchased from culture collections, with a further 40 isolated from WWW plants located in the Barossa Valley and McLaren Vale regions. -
An Assay Redesign and Evaluation
Deficiencies in the current assays for the detection and identification of DNA viruses of carp: an assay redesign and evaluation. David Stone1, Peng Jia2 and Hong Liu2 1Cefas Weymouth Laboratory, UK 2Shenzhen Exit & Entry Inspection and Quarantine Bureau, People's Republic of China. World Class Science for the Marine and Freshwater Environment Overview • BREXIT • Cyprinivirus-specific primers • Failures in CyHV-3 detection using the Gilad qPCR assay • Design and initial evaluation of a CyHV-3 pol qPCR assay • CEV • Current PCR based assays • Failures in the Cefas conventional PCR assay • Design and initial evaluation of a modified nested PCR assay • Work to be done KHV (Cyprinid herpesvirus 3) • Large DNA virus (295 kbp genome) – of the Alloherpesviridae family in the order Herpesvirales • CyHV-3 (Koi herpesvirus - KHV) is the type species of the Cyprinivirus genus -also contains Cyprinid herpesviruses 1 & 2 and Anguillid herpesvirus • Disease affects Common carp (Cyprinus carpio), including ornamental koi carp and varieties and hybrids such as mirror and ghost carp. Goldfish (Carassius auratus) x common carp hybrids also have low susceptibility to CyHV-3 infection Cyprinivirus- specific DNA polymerase primers Nested conventional PCR assay based on CyHV 1-3 DNA polymerase sequences • Analytical sensitivity of 1-10 copies/reaction (~DNA from 0.25mg tissue) • Assay accredited to ISO 17025 Initially run in parallel to the TK primers recommended by the OIE. In the UK the assay was adopted as the primary assay for confirmation of disease outbreaks -
Bacillus Safensis FO-36B and Bacillus Pumilus SAFR-032: a Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates
bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: A Whole Genome 2 Comparison of Two Spacecraft Assembly Facility Isolates 3 Madhan R Tirumalai1, Victor G. Stepanov1, Andrea Wünsche1, Saied Montazari1, 4 Racquel O. Gonzalez1, Kasturi Venkateswaran2, George. E. Fox1§ 5 1Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001. 6 2 Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California 7 Institute of Technology, Pasadena, CA, 91109. 8 9 §Corresponding author: 10 Dr. George E. Fox 11 Dept. Biology & Biochemistry 12 University of Houston, Houston, TX 77204-5001 13 713-743-8363; 713-743-8351 (FAX); email: [email protected] 14 15 Email addresses: 16 MRT: [email protected] 17 VGS: [email protected] 18 AW: [email protected] 19 SM: [email protected] 20 ROG: [email protected] 21 KV: [email protected] 22 GEF: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide 24 resistance, genome comparison, phage insertions 25 26 Background 27 Microbial persistence in built environments such as spacecraft cleanroom facilities [1-3] is often 28 characterized by their unusual resistances to different physical and chemical factors [1, 4-7].