C.V. Didier RAOULT
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Hplc-Uv Quantitation of Folate Synthesized by Rickettsia
HPLC-UV QUANTITATION OF FOLATE SYNTHESIZED BY RICKETTSIA ENDOSYMBIONT IXODES PACIFICUS (REIP) By Junyan Chen A Thesis Presented to The Faculty of Humboldt State University In Partial Fulfillment of the Requirements for the Degree Master of Science in Biology Committee Membership Dr. Jianmin Zhong, Committee Chair Dr. David S. Baston, Committee Member Dr. Jenny Cappuccio, Committee Member Dr. Jacob Varkey, Committee Member Dr. Erik Jules, Program Graduate Coordinator December 2017 ABSTRACT HPLC-UV QUANTITATION OF FOLATE SYNTHESIZED BY RICKETTSIA ENDOSYMBIONT IXODES PACIFICUS (REIP) Junyan Chen Ticks are the most important vector of many infectious diseases in the United States. Understanding the nature of the relationship between Rickettsia endosymbiont Ixodes pacificus (REIP) and Exudes pacificus will help develop strategies for the control of tick- borne diseases, such as Lyme disease, and Rocky Mountain spotted fever. Folate, also known as vitamin B9, is a necessary vitamin for tick survival, and plays a central role in one-carbon metabolism in cells. Folate exist as a large family of structurally related forms that transfer one-carbon groups among biomolecules that are important to cell growth, differentiation, and survival. In Dr. Zheng’s lab, REIP were cultured in Ixodes scapularis embryonic tick cell line ISE6. Previous research has shown that REIP in Ixodes pacificus carries all five de novo folate biosynthesis genes. Folate biosynthesis mRNAs were detected and all recombinant rickettsial folate proteins were overexpressed. To determine whether REIP synthesize folate, we sought to measure the folate concentration in REIP using HPLC-UV quantification with a Diamond HydrideTM liquid chromatography column. 5-methyltetrahydrofolate (5-MTHF), the active circulating form of folate in bacteria was detected. -
Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
E. Coli (Expec) Among E
Elucidating the Unknown Ecology of Bacterial Pathogens from Genomic Data Tristan Kishan Seecharran A thesis submitted in partial fulfilment of the requirements of Nottingham Trent University for the degree of Doctor of Philosophy June 2018 Copyright Statement I hereby declare that the work presented in this thesis is the result of original research carried out by the author, unless otherwise stated. No material contained herein has been submitted for any other degree, or at any other institution. This work is an intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights. Tristan Kishan Seecharran i Acknowledgements I would like to express my sincere gratitude and thanks to my external advisor Alan McNally and director of studies Ben Dickins for their continued support, guidance and encouragement, and without whom, the completion of this thesis would not have been possible. Many thanks also go to the members of the Pathogen Research Group at Nottingham Trent University. I would like to thank Gina Manning and Jody Winter in particular for their invaluable advice and contributions during lab meetings. I would also like to thank our collaborators, Mikael Skurnik and colleagues from the University of Helsinki and Jukka Corander from the University of Oslo, for their much-appreciated support and assistance in this project and the published work on Yersinia pseudotuberculosis. -
BD-CS-057, REV 0 | AUGUST 2017 | Page 1
EXPLIFY RESPIRATORY PATHOGENS BY NEXT GENERATION SEQUENCING Limitations Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi. The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Additional respiratory pathogens to those reported cannot be excluded in samples with ‘Reduced Analytical Sensitivity’. Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases. Validated Organisms BACTERIA Achromobacter -
Evolutionary Origin of Insect–Wolbachia Nutritional Mutualism
Evolutionary origin of insect–Wolbachia nutritional mutualism Naruo Nikoha,1, Takahiro Hosokawab,1, Minoru Moriyamab,1, Kenshiro Oshimac, Masahira Hattoric, and Takema Fukatsub,2 aDepartment of Liberal Arts, The Open University of Japan, Chiba 261-8586, Japan; bBioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; and cCenter for Omics and Bioinformatics, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8561, Japan Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved June 3, 2014 (received for review May 20, 2014) Obligate insect–bacterium nutritional mutualism is among the insects, generally conferring negative fitness consequences to most sophisticated forms of symbiosis, wherein the host and the their hosts and often causing hosts’ reproductive aberrations to symbiont are integrated into a coherent biological entity and un- enhance their own transmission in a selfish manner (7, 8). Re- able to survive without the partnership. Originally, however, such cently, however, a Wolbachia strain associated with the bedbug obligate symbiotic bacteria must have been derived from free-living Cimex lectularius,designatedaswCle, was shown to be es- bacteria. How highly specialized obligate mutualisms have arisen sential for normal growth and reproduction of the blood- from less specialized associations is of interest. Here we address this sucking insect host via provisioning of B vitamins (9). Hence, it –Wolbachia evolutionary -
Legionella Shows a Diverse Secondary Metabolism Dependent on a Broad Spectrum Sfp-Type Phosphopantetheinyl Transferase
Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase Nicholas J. Tobias1, Tilman Ahrendt1, Ursula Schell2, Melissa Miltenberger1, Hubert Hilbi2,3 and Helge B. Bode1,4 1 Fachbereich Biowissenschaften, Merck Stiftungsprofessur fu¨r Molekulare Biotechnologie, Goethe Universita¨t, Frankfurt am Main, Germany 2 Max von Pettenkofer Institute, Ludwig-Maximilians-Universita¨tMu¨nchen, Munich, Germany 3 Institute of Medical Microbiology, University of Zu¨rich, Zu¨rich, Switzerland 4 Buchmann Institute for Molecular Life Sciences, Goethe Universita¨t, Frankfurt am Main, Germany ABSTRACT Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict Submitted 29 June 2016 some novel compounds that are probably involved in cell-cell communication, Accepted 25 October 2016 Published 24 November 2016 differing to known communication systems. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
MARSEILLE Name Surname H-Index Hindex 10 Years Total Publications
MARSEILLE Name Surname h-index hindex 10 years Total publications RAOULT Didier 77 55 1361 MALISSEN Bernard 62 31 277 VIVIER Eric 51 39 175 CAMBILLAU Christian 49 32 221 OLIVE Daniel 49 25 338 FOURNIER Pierre Edouard 42 38 248 HENRISSAT Bernard 38 36 129 DRANCOURT Michel 37 27 229 GORVEL Jean Pierre 37 23 141 TRAPE Jean François 37 20 162 BOURNE Yves 35 8 88 BROUQUI Philippe 33 22 236 CHIMINI Giovanna 33 22 91 LA SCOLA Bernard 31 27 134 MEGE Jean Louis 31 21 180 MOATTI Jean Paul 30 24 295 de LAMBALLERIE Xavier 29 27 168 PONTAROTTI Pierre 29 13 92 CANARD Bruno 28 28 129 de MICCO Philippe 28 20 226 TAMALET Catherine 28 16 191 BLIN Olivier 27 8 198 PAPAZIAN Laurent 27 17 136 CHARREL Remi 22 19 97 FENOLLAR Florence 22 21 99 PAROLA Philippe 22 21 173 ROLAIN Jean Marc 22 21 164 STEIN Andreas 22 11 53 EWBANK Jonathan 20 20 46 PARZY Daniel 20 16 100 ROGIER Christophe 20 18 130 BIAGINI Philippe 19 15 59 OBADIA Yolande 18 14 92 DAVOUST Bernard 15 15 81 GHIGO Eric 14 13 26 DALOD Marc 13 12 30 PIERRE Philippe 13 13 25 SIMON Fabrice 9 7 38 LESCAR Julien 6 6 11 DESNUES Christelle 5 5 12 SIGNOLI Michel 5 5 23 NICE Nom Prénom hindex total hindex 10ans Total publications DELLAMONICA Pierre 27 17 395 HOFMAN Paul 23 12 249 BARBRY Pascal 21 12 57 GLAICHENHAUS Nicolas 21 16 45 LEMICHEZ Emmanuel 16 11 43 MARSEILLE Scientific and Research Activities Short CV from the main investigators of the project with a h-index equal or higher to 20 Last 5 years period Summary of research activities Name: Raoult Surname: Didier Birth date: 1952 Email: [email protected] Affiliation: URMITE, UMR 6236, IRD-198, Marseille Position PU-PH, (MD, PhD, Professor) Scientific Activities PhD training: 38 International lectures for 5 years: 160 Editorial activities: Editor in chief Clinical Microbiology and Infection, Associated Editor Emerging Infectious Diseases, PloS Neglected tropical Diseases, Eur. -
The Risk to Human Health from Free-Living Amoebae Interaction with Legionella in Drinking and Recycled Water Systems
THE RISK TO HUMAN HEALTH FROM FREE-LIVING AMOEBAE INTERACTION WITH LEGIONELLA IN DRINKING AND RECYCLED WATER SYSTEMS Dissertation submitted by JACQUELINE MARIE THOMAS BACHELOR OF SCIENCE (HONOURS) AND BACHELOR OF ARTS, UNSW In partial fulfillment of the requirements for the award of DOCTOR OF PHILOSOPHY in ENVIRONMENTAL ENGINEERING SCHOOL OF CIVIL AND ENVIRONMENTAL ENGINEERING FACULTY OF ENGINEERING MAY 2012 SUPERVISORS Professor Nicholas Ashbolt Office of Research and Development United States Environmental Protection Agency Cincinnati, Ohio USA and School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Professor Richard Stuetz School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Doctor Torsten Thomas School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia ORIGINALITY STATEMENT '1 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 material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom 1 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.' Signed ~ ............................ -
Mariem Joan Wasan Oloroso
Interactions between Arcobacter butzleri and free-living protozoa in the context of sewage & wastewater treatment by Mariem Joan Wasan Oloroso A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Environmental Health Sciences School of Public Health University of Alberta © Mariem Joan Wasan Oloroso, 2021 Abstract Water reuse is increasingly becoming implemented as a sustainable water management strategy in areas around the world facing freshwater shortages and nutrient discharge limits. However, there are a host of biological hazards that must be assessed prior to and following the introduction of water reuse schemes. Members of the genus Arcobacter are close relatives to the well-known foodborne campylobacter pathogens and are increasingly being recognized as emerging human pathogens of concern. Arcobacters are prevalent in numerous water environments due to their ability to survive in a wide range of conditions. They are particularly abundant in raw sewage and are able to survive wastewater treatment and disinfection processes, which marks this genus as a potential pathogen of concern for water quality. Because the low levels of Arcobacter excreted by humans do not correlate with the high levels of Arcobacter spp. present in raw sewage, it was hypothesised that other microorganisms in sewage may amplify the growth of Arcobacter species. There is evidence that Arcobacter spp. survive both within and on the surface of free-living protozoa (FLP). As such, this thesis investigated the idea that Arcobacter spp. may be growing within free-living protozoa also prevalent in raw sewage and providing them with protection during treatment and disinfection processes. -
Diapositive 1
29.04.2013 ESCMID-BERLIN «Culturomics» © by author ESCMID Online Lecture Library Didier Raoult Marseille - France [email protected] www.mediterranee-infection.com As samples in 2012 We received -220,000 samples for culture (bactéria, fungi, viruses) - 200,000 PCR were performed - 115,000 serological testing were tested © by author Real-time laboratory surveillance of sexually-transmissible infections in Marseille University hospitals reveals rise of gonorrhea, syphilis and HIV seroconversions in 2012. PhilippeESCMID Colson1,2 , Frédérique Online Gouriet1,2 Lecture , Sékéné Badiaga 2,3Library, Catherine Tamalet 1,2, Andreas Stein2,4, Didier Raoult1,2 *. Eurosurveillance 2013 2 Culture has been negleted in clinical microbiology, very few new media have been recently very few introduced but it is still central for: Causality Suceptibility testing Genome sequencing© by author ESCMID Online Lecture Library Pathophysiology 3 NEW IDENTIFICATIONS Helicobacter pylori • Peptic ulcer disease • Cancer of the stomach, grown in 1983 © by author ESCMIDSeen sinceOnline the Lecture 19th century Library 4 © by author ESCMID Online Lecture Library 5 PROGRESSES MADE IN MICROBIOLOGY FROM 1979 TO 2012 THANKS TO THE DEVELOPMENT OF NEW TECHNOLOGIES © by author a) the ESCMIDleft ordinate axis refers toOnline the cumulative numbers Lecture of bacterial species Library with validly published names (green curve); the right ordinate axis refers to the cumulative numbers of sequenced bacterial genomes (purple) and sequenced viral genomes (blue); 6 © by author b) the left ordinate axis refers to the numbers of articles containing “metagenome” as keyword (red) and of articles containing “microbiota” as keyword (grey); the right ordinate axisESCMID refers to the numbers Online of articles containing Lecture “MALDI-TOF” andLibrary “clinical microbiology” as keywords (orange). -
Preliminary Programme
PRELIMINARY PROGRAMME PARIS 2015 EVOLUTION IN LABORATORY MEDICINE 21st IFCC - EFLM European Congress of Clinical Chemistry and Laboratory Medicine EuroMedLab JIB 2015 exhibition 22 -24 June 2015 Paris, France Palais des Congrès 21-25 June 2015 DATES TO FOCUS ON 1 February 2015 POSTER ABSTRACT DEADLINE 30 April 2015 DEADLINE FOR REDUCED FEES REGISTRATION The Preliminary Programme has been released in September 2014. Any further update is available at: www.www.paripariss 2015.o2015.orr g g CONTENTSCONTENTS Auspices 4 Invitations 5 Committees 12 Executive Boards 14 Congress Secretariat 15 Week agenda 16 Opening Ceremony 18 Scientific Programme 19 Educational workshops 28 SDB sessions 29 Satellite meetings 30 Abstract submission 31 Social events 33 General information 34 Registration 37 Hotel information 39 Practical information 40 3 AUSAUSPICESPICES Asia-Pacific Federation for Clinical Biochemistry and Laboratory Medicine (APFCB) 4 IINVNVIITATTATIIONON -- CongressCongress OrganisingOrganising CommitteeCommittee ChairChair Dear Colleagues and Friends, On behalf of the Congress Organising Committee, it is a great pleasure to invite you all, specialists in Lab Medicine and partners, to EuroMedLab Paris 2015, the 21st IFCC-EFLM European Congress of Clinical Chemistry and Laboratory Medicine. For the first time, this congress, including the Journées Internationales de Biologie (JIB), takes place in Paris, France, on June 21-25 2015 in the Palais des Congrès, one of the capital’s legendary venue. All around the world, health care systems are facing some of their greatest challenges and all nations need to find better, more innovative ways to treat and prevent illness. The coupling of science-technology and clinical medicine remains the relentless driver of new questions.