Attachment 1 .PLOS ONE
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
The Role of Earthworm Gut-Associated Microorganisms in the Fate of Prions in Soil
THE ROLE OF EARTHWORM GUT-ASSOCIATED MICROORGANISMS IN THE FATE OF PRIONS IN SOIL Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Taras Jur’evič Nechitaylo aus Krasnodar, Russland 2 Acknowledgement I would like to thank Prof. Dr. Kenneth N. Timmis for his guidance in the work and help. I thank Peter N. Golyshin for patience and strong support on this way. Many thanks to my other colleagues, which also taught me and made the life in the lab and studies easy: Manuel Ferrer, Alex Neef, Angelika Arnscheidt, Olga Golyshina, Tanja Chernikova, Christoph Gertler, Agnes Waliczek, Britta Scheithauer, Julia Sabirova, Oleg Kotsurbenko, and other wonderful labmates. I am also grateful to Michail Yakimov and Vitor Martins dos Santos for useful discussions and suggestions. I am very obliged to my family: my parents and my brother, my parents on low and of course to my wife, which made all of their best to support me. 3 Summary.....................................................………………………………………………... 5 1. Introduction...........................................................................................................……... 7 Prion diseases: early hypotheses...………...………………..........…......…......……….. 7 The basics of the prion concept………………………………………………….……... 8 Putative prion dissemination pathways………………………………………….……... 10 Earthworms: a putative factor of the dissemination of TSE infectivity in soil?.………. 11 Objectives of the study…………………………………………………………………. 16 2. Materials and Methods.............................…......................................................……….. 17 2.1 Sampling and general experimental design..................................................………. 17 2.2 Fluorescence in situ Hybridization (FISH)………..……………………….………. 18 2.2.1 FISH with soil, intestine, and casts samples…………………………….……... 18 Isolation of cells from environmental samples…………………………….………. -
Margaret A. Highland, DVM Washington State University
Bacterial Pneumonia in Sheep, The Domestic – Bighorn Sheep Interface, and Research at ADRU USAHA Committee on Sheep and Goats Providence, RI October 27, 2015 PLC M. A. Highland, DVM, DACVP, PhD candidate PhD Veterinary Training Program USDA-ARS ADRU Veterinary Microbiology and Pathology Washington State University Pullman, WA DS – BHS Interface Issue Captive/penned commingling studies & anecdotal field reports associate BHS and DS contact with BHS pneumonia Removal of DS public land grazing allotments - profound economic impacts Pneumonia continues to afflict BHS herds - despite decades of research and intense management practices Anecdotal field reports also associate DG with BHS pneumonia - pack goat restrictions on public lands DS and BHS Pneumonia DS . Lambs > Adults . Etiology • Polymicrobial (bacteria +/- viruses) or Unimicrobial • Multifactorial (colostrum, air quality, environmental stressors) BHS (wild) . Reports of respiratory disease date back to the 1920’s . All age outbreaks +/- subsequent years of disease in lambs → population-limiting disease . Etiology • Long been debated • Evidence for polymicrobial (bacterial) and multifactorial • Viruses occasionally reported (no current indication for primary role) What do we know about BHS (and DS) pneumonia? Polymicrobial and Multifactorial (the presence of the bacteria in BHS alone does NOT = disease/death) Incompletely understood disease phenomenon DS and BHS pneumonia-associated bacteria Mycoplasma ovipneumoniae (M ovi) Pasteurellaceae (“Pasteurellas”) . Mannheimia haemolytica -
Engineering the Genome of Minimal Bacteria Using CRISPR/Cas9 Tools Iason Tsarmpopoulos
Engineering the genome of minimal bacteria using CRISPR/Cas9 tools Iason Tsarmpopoulos To cite this version: Iason Tsarmpopoulos. Engineering the genome of minimal bacteria using CRISPR/Cas9 tools. Mi- crobiology and Parasitology. Université de Bordeaux, 2017. English. NNT : 2017BORD0787. tel- 01834971 HAL Id: tel-01834971 https://tel.archives-ouvertes.fr/tel-01834971 Submitted on 11 Jul 2018 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. THÈSE PRÉSENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE BORDEAUX ÉCOLE DOCTORALE Science de la vie et de la Santé SPÉCIALITÉ Microbiologie and Immunologie Par Iason TSARMPOPOULOS Ingénierie de génome de bactéries minimales par des outils CRISPR/Cas9 Sous la direction de : Monsieur Pascal SIRAND-PUGNET Soutenue le jeudi 07 décembre 2017 à 14h00 Lieu : INRA, 71 avenue Edouard Bourlaux 33882 Villenave d'Ornon salle Amphithéâtre Josy et Colette Bové Membres du jury : Mme Cécile BEBEAR Université de Bordeaux et CHU de Bordeaux Président Mme Florence TARDY Anses-Laboratoire de Lyon Rapporteur M. Matthieu JULES Institut Micalis, INRA and AgroParisTech Rapporteur M. David BIKARD Institut Pasteur Examinateur M. Fabien DARFEUILLE INSERM U1212 - CNRS UMR 5320 Invité Mme Carole LARTIGUE-PRAT INRA - Université de Bordeaux Invité M. -
Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed. -
Effects of Respiratory Disease on Kele Piglets Lung Microbiome, Assessed Through 16S Rrna Sequencing
Veterinary World, EISSN: 2231-0916 RESEARCH ARTICLE Available at www.veterinaryworld.org/Vol.13/September-2020/31.pdf Open Access Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing Jing Zhang , Kaizhi Shi , Jing Wang , Xiong Zhang , Chunping Zhao , Chunlin Du and Linxin Zhang Key Laboratory of Livestock and Poultry Major Epidemic Disease Monitoring and Prevention , Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China. Corresponding author: Kaizhi Shi, e-mail: [email protected] Co-authors: JZ: [email protected], JW: [email protected], XZ: [email protected], CZ: [email protected], CD: [email protected], LZ: [email protected] Received: 19-05-2020, Accepted: 07-08-2020, Published online: 25-09-2020 doi: www.doi.org/10.14202/vetworld.2020.1970-1981 How to cite this article: Zhang J, Shi K, Wang J, Zhang X, Zhao C, Du C, Zhang L (2020) Effects of respiratory disease on Kele piglets lung microbiome, assessed through 16S rRNA sequencing, Veterinary World, 13(9): 1970-1981. Abstract Background and Aim: Due to the incomplete development of the immune system in immature piglets, the respiratory tract is susceptible to invasion by numerous pathogens that cause a range of potential respiratory diseases. However, few studies have reported the changes in pig lung microorganisms during respiratory infection. Therefore, we aimed to explore the differences in lung environmental microorganisms between healthy piglets and piglets with respiratory diseases. Materials and Methods: Histopathological changes in lung sections were observed in both diseased and healthy pigs. Changes in the composition and abundance of microbiomes in alveolar lavage fluid from eleven 4-week-old Chinese Kele piglets (three clinically healthy and eight diseased) were studied by IonS5TM XL sequencing of the bacterial 16S rRNA genes. -
Examining the Risk of Disease Transmission Between Wild Dall's
Examining the Risk of Disease Transmission between Wild Dall’s Sheep and Mountain Goats, and Introduced Domestic Sheep, Goats, and Llamas in the Northwest Territories Prepared for: The Northwest Territories Agricultural Policy Framework and Environment and Natural Resources Government of the Northwest Territories, Canada August 20, 2005 Examining the Risk of Disease Transmission between Wild Dall’s Sheep and Mountain Goats, and Introduced Domestic Sheep, Goats, and Llamas in the Northwest Territories Elena Garde 1,2 , Susan Kutz 1,3 , Helen Schwantje 4, Alasdair Veitch 5, Emily Jenkins 1,6 , Brett Elkin 7 1 Research Group for Arctic Parasitology and the Canadian Cooperative Wildlife Health Centre, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4. 2 Associate Wildlife Veterinarian, Biodiversity Branch, Ministry of Environment, PO Box 9338, Stn Prov Govt, 2975 Jutland Road, Victoria, BC, V8W 9M1, (250) 953-4285 [email protected] 3 Associate Professor, Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary AB, T2N 4N1 Ph: (306) 229-6110 4 Wildlife Veterinarian, Biodiversity Branch, Ministry of Environment, PO Box 9338, Stn Prov Govt, 2975 Jutland Road, Victoria, BC, V8W 9M1, (250) 953-4285 [email protected] 5 Supervisor, Wildlife Management, Environment and Natural Resources, Sahtu Region, P.O. Box 130, Norman Wells, NT X0E 0V0, Ph: (867) 587-2786; Fax: (867) 587-2359 [email protected] 6 Wildlife Disease Specialist / Research Scientist, Canadian Wildlife Service, 115 Perimeter Rd. Saskatoon, SK S7N 0X4 (306) 975-5357, (306) 966-7246 7 Disease & Contaminants Specialist, Environment and Natural Resources, 500 – 6102 50 th Ave. -
Genomes Published Outside of SIGS, June
Standards in Genomic Sciences (2011) 5:154-167 DOI:10.4056/sigs.2324675 Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June – September 2011 Oranmiyan W. Nelson1 and George M. Garrity1 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bib- liometric data for such references to the SIGS editorial office. Phylum Crenarchaeota Phylum Euryarchaeota Pyrococcus yayanosii CH1, sequence accession CP002779 [1] Methanocella paludicola, sequence accession AP011532 [2] Halorhabdus tiamatea, sequence accession AFNT00000000 [3] Thermococcus sp. Strain 4557, sequence accession CP002920 [4] Phylum Chloroflexi Phylum Proteobacteria Ralstonia solanacearum strain Po82, sequence accession CP002819 (chromosome) and CP002820 (megaplasmid) [5 Desulfovibrio alaskensis G20, sequence accession CP000112 [6] Methylophaga aminisulfidivorans MPT, sequence accession AFIG00000000 [7] Acinetobacter sp. P8-3-8, sequence accession AFIE00000000 [8] Sphingomonas strain KC8, sequence accession AFMP01000000 -
A Pilot Study of the Effects of Mycoplasma Ovipneumoniae Exposure on Domestic Lamb Growth And
bioRxiv preprint doi: https://doi.org/10.1101/459628; this version posted November 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Full title: 2 A pilot study of the effects of Mycoplasma ovipneumoniae exposure on domestic lamb growth and 3 performance. 4 5 Thomas E. Besser1*, Jessica Levy1, Melissa Ackerman2, Danielle Nelson1, Kezia Manlove3, Kathleen A. 6 Potter1, Jan Busboom4, Margaret Benson4 7 8 Short title: 9 Sub-clinical Mycoplasma ovipneumoniae infection 10 11 1 Department of Veterinary Microbiology and Pathology, Washington State University College of 12 Veterinary Medicine, Pullman WA, United States of America 13 2 Department of Veterinary Clinical Sciences, Washington State University College of Veterinary 14 Medicine, Pullman WA, United States of America 15 3 Department of Wildland Resources, Utah State University College of Natural Resources, Logan UT, 16 United States of America 17 4 Department of Animal Sciences, Washington State University College of Agricultural, Human, and 18 Natural Resource Sciences, Pullman WA, United States of America. 19 * Corresponding author 20 E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/459628; this version posted November 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. -
Mycoplasma Ovipneumoniae Rotter ML, Hirschl AM
RESEARCH LETTERS Figure. Direct examination with dark-field microscopy of specimens from a patient with agammaglobulinemia who had Spiroplasma apis infection, France. A) Helical and motile bacteria in blood culture. B) Elongated and coccoid bacteria in joint fluid. C) Helical and motile bacteria in culture from joint fluid in modified SP4 broth medium. Scale bar indicates 10 µm. than honeybees. The insect stings in this patient are a likely 7. Mueller NJ, Tini GM, Weber A, Gaspert A, Husmann L, gateway of the reported infection. Bloemberg G, et al. Hepatitis from Spiroplasma sp. in an immunocompromised patient. Am J Transplant. 2015;15:2511–6. In summary, clinicians and microbiologists should be http://dx.doi.org/10.1111/ajt.13254 aware of fastidious organisms in atypical infections in im- 8. Lorenz B, Schroeder J, Reischl U. First evidence of an endogenous munocompromised patients. Our findings indicate a need Spiroplasma sp. infection in humans manifesting as unilateral for prolonged culture on specific agar on all joint fluids in cataract associated with anterior uveitis in a premature baby. Graefes Arch Clin Exp Ophthalmol. 2002;240:348–53. patients with agammaglobulinemia and targeted molecular http://dx.doi.org/10.1007/s00417-002-0453-3 methods to identify S. apis organisms. 9. Aquilino A, Masiá M, López P, Galiana AJ, Tovar J, Andrés M, et al. First human systemic infection caused by Spiroplasma. J Clin Microbiol. 2015;53:719–21. http://dx.doi.org/10.1128/JCM.02841-14 Acknowledgments We thank Anne Laurence Thomi Georgelin, who referred the Address for correspondence: Olivier Lortholary, Necker-Enfants Malades patient to the Necker-Pasteur Center for Infectious Diseases and University Hospital, 149 rue de Sevre 75743, Paris CEDEX, France; Tropical Medicine; Valérie Zeller for the management of septic email: [email protected] polyarthritis; and Philippe Lanotte and Marie-Pierre Dubrana, who participated in molecular analysis. -
( 12 ) United States Patent
US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U . -
A Review of Ureaplasma Diversum: a Representative of the Mollicute Class Associated with Reproductive and Respiratory Disorders in Cattle
REVIEW published: 18 February 2021 doi: 10.3389/fvets.2021.572171 A Review of Ureaplasma diversum: A Representative of the Mollicute Class Associated With Reproductive and Respiratory Disorders in Cattle Manoel Neres Santos Junior 1,2, Nayara Silva de Macêdo Neres 1, Guilherme Barreto Campos 1, Bruno Lopes Bastos 1, Jorge Timenetsky 3 and Lucas Miranda Marques 1,2,3* 1 Department of Biointeraction, Multidisciplinary Institute of Health, Universidade Federal da Bahia, Vitória da Conquista, Brazil, 2 Department of Microbiology, State University of Santa Cruz (UESC), Ilhéus, Brazil, 3 Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil The Mollicutes class encompasses wall-less microbes with a reduced genome. They may infect plants, insects, humans, and animals including those on farms and in livestock. Edited by: Ureaplasma diversum is a mollicute associated with decreased reproduction mainly in the Michael Kogut, conception rate in cattle, as well as weight loss and decreased quality in milk production. United States Department of Agriculture, United States Therefore, U. diversum infection contributes to important economic losses, mainly in Reviewed by: large cattle-producing countries such as the United States, China, Brazil, and India. Marie Rene Culhane, The characteristics of Mollicutes, virulence, and pathogenic variations make it difficult to University of Minnesota, United States control their infections. Genomic analysis, prevalence studies, and immunomodulation Christine Letitia -
Isolation and Molecular Characterization of Mycoplasma Spp
Veterinary World, EISSN: 2231-0916 RESEARCH ARTICLE Available at www.veterinaryworld.org/Vol.12/May-2019/6.pdf Open Access Isolation and molecular characterization of Mycoplasma spp. in sheep and goats in Egypt Mounier M. Abdel Halium1, Fayez A. Salib1, S. A. Marouf2 and Emil S. Abdel Massieh1 1. Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt; 2. Department of Microbiology and Mycology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt. Corresponding author: Emil S. Abdel Massieh, e-mail: [email protected] Co-authors: MMAH: [email protected], FAS: [email protected], SAM: [email protected] Received: 04-12-2018, Accepted: 15-03-2019, Published online: 13-05-2019 doi: 10.14202/vetworld.2019.664-670 How to cite this article: Abdel Halium MM, Salib FA, Marouf SA, Abdel Massieh ES (2019) Isolation and molecular characterization of Mycoplasma spp. in sheep and goats in Egypt, Veterinary World, 12(5): 664-670. Abstract Background and Aim: Different species of Mycoplasma are associated with many pathological problems in small ruminants including respiratory manifestation, this problem results in significant losses, especially in African countries. This study aimed to (I) study some epidemiological aspects of Mycoplasma species infections in Egyptian sheep and goats at Giza Governorate, (II) diagnosis of Mycoplasma species affections using bacterial isolation and identification, (III) apply the polymerase chain reaction (PCR) for typing of different Mycoplasma species, and (IV) illustrate the phylogenetic tree for the isolated Mycoplasma species and other species from GenBank using the purified PCR product. Materials and Methods: A total of 335 samples were collected from sheep and goats from Giza Governorate in Egypt as 142 nasal swabs from clinically affected animals, 167 pneumonic lungs, 18 samples from tracheal bifurcation, and 8 samples by bronchial wash were cultured on pleuropneumonia-like organisms (PPLOs) media for cultivation of Mycoplasma species.