Invivogen Insight Newsletter: Mycoplasma
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Mycoplasma Agalactiae MEMBRANE PROTEOME
UNIVERSITÀ DEGLI STUDI DI SASSARI SCUOLA DI DOTTORATO IN SCIENZE BIOMOLECOLARI E BIOTECNOLOGICHE INDIRIZZO MICROBIOLOGIA MOLECOLARE E CLINICA XXIII Ciclo CHARACTERIZATION OF Mycoplasma agalactiae MEMBRANE PROTEOME Direttore: Prof. Bruno Masala Tutor: Dr. Alberto Alberti Tesi di dottorato della Dott.ssa Carla Cacciotto ANNO ACCADEMICO 2009-2010 TABLE OF CONTENTS 1. Abstract 2. Introduction 2.1 Mycoplasmas: taxonomy and main biological features 2.2 Metabolism 2.3 In vitro cultivation 2.4 Mycoplasma lipoproteins 2.5 Invasivity and pathogenicity 2.6 Diagnosis of mycoplasmosis 2.7 Mycoplasma agalactiae and Contagious Agalactia 3. Research objectives 4. Materials and methods 4.1 Media and buffers 4.2 Bacterial strains and culture conditions 4.3 Total DNA extraction and PCR 4.4 Total proteins extraction 4.5 Triton X-114 fractionation 4.6 SDS-PAGE 4.7 Western immunoblotting 4.8 2-D PAGE 4.9 2D DIGE 4.10 Spot picking and in situ tryptic digestion 4.11 GeLC-MS/MS 4.12 MALDI-MS 4.13 LC-MS/MS 4.14 Data analysis Dott.ssa Carla Cacciotto, Characterization of Mycoplasma agalactiae membrane proteome. Tesi di Dottorato in Scienze Biomolecolari e Biotecnologiche, Università degli Studi di Sassari. 5. Results 5.1 Species identification 5.2 Extraction of bacterial proteins and isolation of liposoluble proteins 5.3 2-D PAGE/MS of M. agalactiae PG2T liposoluble proteins 5.4 2D DIGE of liposoluble proteins among the type strain and two field isolates of M. agalactiae 5.5 GeLC-MS/MS of M. agalactiae PG2T liposoluble proteins 5.6 Data analysis and classification 6. Discussion 7. -
( 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 Phylogenetic Analysis of the Mycoplasmas: Basis for Their Lc Assification W
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@University of Nebraska University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Public Health Resources Public Health Resources 9-1989 A Phylogenetic Analysis of the Mycoplasmas: Basis for Their lC assification W. G. Weisburg University of Illinois J. G. Tully National Institute of Allergy and Infectious Diseases D. L. Rose National Institute of Allergy and Infectious Diseases J. P. Petzel Iowa State University H. Oyaizu University of Illinois See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/publichealthresources Weisburg, W. G.; Tully, J. G.; Rose, D. L.; Petzel, J. P.; Oyaizu, H.; Yang, D.; Mandelco, L.; Sechrest, J.; Lawrence, T. G.; Van Etten, James L.; Maniloff, J.; and Woese, C. R., "A Phylogenetic Analysis of the Mycoplasmas: Basis for Their lC assification" (1989). Public Health Resources. 310. https://digitalcommons.unl.edu/publichealthresources/310 This Article is brought to you for free and open access by the Public Health Resources at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Public Health Resources by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors W. G. Weisburg, J. G. Tully, D. L. Rose, J. P. Petzel, H. Oyaizu, D. Yang, L. Mandelco, J. Sechrest, T. G. Lawrence, James L. Van Etten, J. Maniloff, and C. R. Woese This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ publichealthresources/310 JOURNAL OF BACTERIOLOGY, Dec. 1989, p. 6455-6467 Vol. 171, No. -
Ureaplasma Urealyticum and Ureaplasma Parvum
The Journal of Molecular Diagnostics, Vol. 13, No. 2, March 2011 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved. DOI: 10.1016/j.jmoldx.2010.10.007 Modified Real-Time PCR for Detecting, Differentiating, and Quantifying Ureaplasma urealyticum and Ureaplasma parvum Ellen Vancutsem,* Oriane Soetens,* microbiological methods and are, therefore, usually re- Maria Breugelmans,† Walter Foulon,† ferred to as Ureaplasma species. They are found in the and Anne Naessens* lower genital tract of nearly 50% of pregnant women as part of the normal vaginal flora. However, in some cases, From the Departments of Microbiology and Infection Control* Ureaplasma species have interfered with normal fetal de- and Obstetrics,† Universitair Ziekenhuis Brussel, Brussels, velopment by causing an ascending infection.2–7 The Belgium reason for this infection is not fully understood but may be associated with the virulence of the microorganism, the host immune system, or local factors present in the lower We evaluated a previously described quantitative real- genital tract. Species differentiation might be important time PCR (qPCR) for quantifying and differentiating because previous studies2,8,9 suggest that nongonococ- Ureaplasma parvum and U. urealyticum. Because of cal urethritis and an adverse pregnancy outcome with nonspecific reactions with Staphylococcus aureus respect to birth weight, gestational age, and preterm DNA in the U. parvum PCR, we developed a modified delivery are implicated with the presence of U. urealyti- qPCR and designed new primers. These oligonucleo- cum and not with U. parvum. tides eradicated cross-reactions, indicating higher Because strains can only be differentiated with la- specificity. -
Mycoplasma Pirum Sp. Nov. a Terminal Structured Mollicute from Cell Cultures
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1985, p. 285-291 Vol. 35, No. 3 0020-7713/85/030285-07$02.00/0 Copyright 0 1985, International Union of Microbiological Societies Mycoplasma pirum sp. nov. a Terminal Structured Mollicute from Cell Cultures RICHARD A. DEL GIUDICE,'" JOSEPH G. TULLY,* DAVID L. ROSE,2 AND ROGER M. COLE3? Diagnostic Microbiology Laboratory, National Cancer Institute-Frederick Cancer Research Facility,' and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases,2 Frederick, Maryland 21 701 and Laboratory of Streptococcal Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 202053 More than 200 mycoplasma isolates recovered from a variety of contaminated cell cultures from 1968 to the present were found to belong to a distinct serological group (serogroup 38). An analysis of representative strains of this collection showed that they possessed all of the characteristics of organisms belonging to the genus Mycoplasma. These organisms were capable of fermenting glucose and of hydrolyzing arginine, and they required cholesterol or serum for growth. These organisms were unusual in that they possessed an organized terminal structure or tip, a morphological structure which has been found in at least six other species in the genus Mycoplasma. These organisms were also serologically distinct from all previously established species in the genus Mycoplasma and the genus Acholeplasma. On the basis of these findings and other morphological, biological, and serological characteristics of the strains recovered, we propose that mycoplasmas with these properties belong to a new species, Mycoplasma pirum sp. nov. Strain HRC 70-159 (= ATCC 25960) is the type strain of this species. -
Table S1. Proportional Abundance, and Absolute Abundance of Penile Bacteria from the 266 Men Included in the HIV Seroconversion Cohort
Table S1. Proportional abundance, and absolute abundance of penile bacteria from the 266 men included in the HIV Seroconversion Cohort. All men were uncircumcised. Proportional Abundance Absolute Abundance (16S copies/swab) Genus Median Q#1 Q#3 Median Q#1 Q#3 Prevotella 0.155 0.059 0.279 2.78E+07 9.78E+05 3.14E+08 Peptoniphilus 0.077 0.038 0.119 1.52E+07 1.66E+06 8.69E+07 Peptoniphilaceae<0.97*† 0.049 0.013 0.125 7.81E+06 2.97E+05 1.39E+08 Porphyromonas 0.032 0.010 0.067 4.47E+06 2.36E+05 9.88E+07 Finegoldia 0.029 0.005 0.104 3.37E+06 7.02E+05 2.07E+07 Corynebacterium 0.027 0.004 0.119 2.74E+06 7.12E+05 1.19E+07 Anaerococcus 0.025 0.008 0.061 4.38E+06 7.03E+05 2.10E+07 Dialister 0.018 0.002 0.045 1.76E+06 7.01E+04 3.40E+07 Lactobacillus 0.002 0.001 0.004 2.46E+05 3.33E+04 2.33E+06 Gardnerella 0.001 0.000 0.003 5.72E+04 9.27E+03 8.40E+05 Ezakiella 0.004 0.001 0.016 3.59E+05 2.59E+04 1.11E+07 Clostridiales incertae sedis XIII<0.97*† 0.003 0.000 0.010 3.80E+05 1.32E+04 1.10E+07 Mobiluncus 0.001 0.000 0.011 2.24E+05 1.18E+04 6.54E+06 Firmicutes<0.97*‡ 0.005 0.001 0.016 4.55E+05 1.76E+04 1.55E+07 Murdochiella 0.004 0.001 0.015 6.34E+05 2.70E+04 1.10E+07 Campylobacter 0.004 0.000 0.013 4.19E+05 1.69E+04 1.25E+07 Negativicoccus 0.003 0.000 0.018 3.83E+05 2.54E+04 6.11E+06 Saccharofermentans<0.97* 0.001 0.000 0.009 9.49E+04 7.09E+03 5.02E+06 Peptostreptococcus 0.004 0.000 0.027 2.13E+05 1.69E+04 1.38E+07 Proteobacteria<0.97*‡ 0.001 0.000 0.010 9.69E+04 7.26E+03 3.90E+06 Porphyromonas<0.97* 0.001 0.000 0.005 1.08E+05 4.03E+03 3.46E+06 Staphylococcus -
Microbiology Catalogue Contents
Microbiology catalogue Contents 3 About ATCC 4 About the ATCC / LGC Standards partnership 5 Quality control strains 7 Pharmaceutical applications 12 Food microbiology 20 Food microbiology, Genomic DNA 21 Water microbiology 24 Catalogue listing 38 Nucleic Acids prepared from ATCC Genuine Cultures® 39 Fully sequenced microbes 45 Microbial technical resource 61 Instructions for rehydrating freeze-dried cultures 63 ATCC MTA All care has been taken in the compilation of the information contained in this catalogue. However, any applications for products are suggestions only, and LGC Standards makes no express or implied representations or warranties regarding the accuracy, content, completeness, or reliability of the information or any suggestions provided, and specifically disclaims any and all implied warranties with respect to the same, including without limitation any warranties of merchantability, fitness or suitability for particular purpose. About ATCC Mission ATCC is a global nonprofit bioresource centre and ATCC is an independent, private, nonprofit research organisation that provides biological biological resource centre (BRC) and research products, technical services and educational organisation. programmes to private industry, government and academic organisations. The mission of As a biological resource centre, ATCC ATCC is to acquire, authenticate, preserve, authenticates microorganisms and cell lines and develop and distribute biological materials, manages logistics of long-term preservation information, technology, intellectual -
Mycoplasma Spermatophilum, a New Species Isolated from Human Spermatozoa and Cervix AURIOL C
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1991, p. 229-233 Vol. 41, No. 2 0020-7713/91/020229-05$02.oo/o Copyright 0 1991, International Union of Microbiological Societies Mycoplasma spermatophilum, a New Species Isolated from Human Spermatozoa and Cervix AURIOL C. HILL Medical Research Council Toxicology Unit, Woodmansterne Road, Carshalton, Surrey SM5 4EF, United Kingdom A mycoplasma isolated from human spermatozoa and a human cervix was shown to be serologically distinct from 98 previously recognized MycopEasma and AchoZepZasma spp. Six mycoplasma colonies were cloned and examined in detail for morphology, growth, and biochemical characteristics; five of these were from sperm samples and one was from a cervix. These strains were closely related and had the following properties: guanine-plus-cytosine content of 32 mol%, requirement for sterol, and anaerobic growth. Glucose was not metabolized, and arginine and urea were not hydrolyzed. Strain AH159 (= NCTC 11720) is the type strain of a new species, Mycoplasma spermatophilum. Twelve named Mycoplasma and Acholeplasma species colony isolated from each patient was cloned to produce a have been isolated from the respiratory or genital tracts of pure culture; this was done by initially filtering a broth humans (6). Mycoplasma buccale, Mycoplasma faucium, culture through a 220-nm-pore-size membrane filter, cultur- Mycoplasma lipophilum , Mycoplasma orale, Mycoplasma ing the filtrate on solid medium, transferring a single result- pneumoniae, and Mycoplasma salivarium are found almost ing colony to another agar plate, and inoculating the subse- exclusively in respiratory tracts. Mycoplasma fermentans quent growth into broth. This whole procedure was repeated has been found infrequently in urogenital tracts, while My- an additional four times; thus, the organisms were filter coplasma primatum, a species commonly present in nonhu- cloned five times (29). -
APUTS) Reporting Terminology and Codes Microbiology (V1.0
AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v1.0) 1 12/02/2013 APUTS Report Information Model - Urine Microbiology Page 1 of 1 Specimen Type Specimen Macro Time Glucose Bilirubin Ketones Specific Gravity pH Chemistry Protein Urobilinogen Nitrites Haemoglobin Leucocyte Esterases White blood cell count Red blood cells Cells Epithelial cells Bacteria Microscopy Parasites Microorganisms Yeasts Casts Crystals Other elements Antibacterial Activity No growth Mixed growth Urine MCS No significant growth Klebsiella sp. Bacteria ESBL Klebsiella pneumoniae Identification Virus Fungi Growth of >10^8 org/L 10^7 to 10^8 organism/L of mixed Range or number Colony Count growth of 3 organisms 19090-0 Culture Organism 1 630-4 LOINC >10^8 organisms/L LOINC Significant growth e.g. Ampicillin 18864-9 LOINC Antibiotics Susceptibility Method Released/suppressed None Organism 2 Organism 3 Organism 4 None Consistent with UTI Probable contamination Growth unlikely to be significant Comment Please submit a repeat specimen for testing if clinically indicated Catheter comments Sterile pyuria Notification to infection control and public health departments PUTS Urine Microbiology Information Model v1.mmap - 12/02/2013 - Mindjet 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 1 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report -
United States Patent (19) 11 Patent Number: 5,824,479 Smida Et Al
O USOO5824479A United States Patent (19) 11 Patent Number: 5,824,479 Smida et al. 45) Date of Patent: Oct. 20, 1998 54 INTER-LINE-PCR Chemical Abstract, vol. 120, 1994, p. 326. Abstract No. 20:976646, 75 Inventors: Jan Smida, Freising; Stefan Leibhard, Chemical Abstract, vol. 118, 1993, p. 562, Abstract No. Oberschleissheim; Ludwig Hieber, 118:56972r. Kirchheim; F. Eckardt-Schupp, Frothingham et al. A PCR-Based Method of Identifying Pfaffenhofen, all of Germany Species-Specific Repeated DNAs, BioTechniques, vol. 13. No. 2, 1992, pp. 210, 212. 213. 73) Assignee: Forschungszentrum fur, Umwelt und Furano et al., Amplification of the Ancient Murine Lx Family Gesundheit GmbH. Oberschleissheim, of Long Interspersed Repeated DNA Occurred During the Germany Murine Radiation, J. Mol. Evol., vol. 38 (1994), pp. 18-27. Pascale et al. The Evolution of Long Interspersed Repeated (21) Appl. No.: 646,809 DNA (L1, LINE 1) as Revealed by the Analysis of an Ancient Rodent Ll DNA Family, J. Mol. Evol. (1993), vol. 36 ppi (22 Filed: May 21, 1996 9-20. 30 Foreign Application Priority Data Gong et al., COMMUNICATION Identification of Region Specific Cosmid Clones by Hybrodization with Pooled May 22, 1995 DEI Germany ........................ 19518769.5 Alu-LINE Polymerase Chain Reaction Products of Yeast (51) int. Cl. ................... C12Q 1/68; C12P 19/34; Artificial Chromosone Clones, Methods in Mol. and Cell. CO7H 21/04 Biol. (1994), 4:269-272. (52) U.S. Cl. ........................... 435/6; 536/24.3: 536/22.1; Laten and Morris. SIRE-1, a long interspersed repetitive 435/91.2 DNA element from soybean with weak sequence similarity to (58) Field of Search ................................. -
Moving Beyond Serovars
ABSTRACT Title of Document: MOLECULAR AND BIOINFORMATICS APPROACHES TO REDEFINE OUR UNDERSTANDING OF UREAPLASMAS: MOVING BEYOND SEROVARS Vanya Paralanov, Doctor of Philosophy, 2014 Directed By: Prof. Jonathan Dinman, Cell Biology and Molecular Genetics, University of Maryland College Park Prof. John I. Glass, Synthetic Biology, J. Craig Venter Institute Ureaplasma parvum and Ureaplasma urealyticum are sexually transmitted, opportunistic pathogens of the human urogenital tract. There are 14 known serovars of the two species. For decades, it has been postulated that virulence is related to serotype specificity. Understanding of the role of ureaplasmas in human diseases has been thwarted due to two major barriers: (1) lack of suitable diagnostic tests and (2) lack of genetic manipulation tools for the creation of mutants to study the role of potential pathogenicity factors. To address the first barrier we developed real-time quantitative PCRs (RT-qPCR) for the reliable differentiation of the two species and 14 serovars. We typed 1,061 ureaplasma clinical isolates and observed about 40% of isolates to be genetic mosaics, arising from the recombination of multiple serovars. Furthermore, comparative genome analysis of the 14 serovars and 5 clinical isolates showed that the mba gene, used for serotyping ureaplasmas was part of a large, phase variable gene system, and some serovars shown to express different MBA proteins also encode mba genes associated with other serovars. Together these data suggests that differential pathogenicity and clinical outcome of an ureaplasmal infection is most likely due to the presence or absence of potential pathogenicity factors in individual ureaplasma clinical isolates and/or patient to patient differences in terms of autoimmunity and microbiome. -
Rapid, Sensitive PCR-Based Detection of Mycoplasmas In
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 1994, p. 953-959 Vol. 60, No. 3 0099-2240/94/$04.00 +0 Copyright © 1994, American Society for Microbiology Rapid, Sensitive PCR-Based Detection of Mycoplasmas in Simulated Samples of Animal Sera OLIVIER DUSSURGET AND DAISY ROULLAND-DUSSOIX* Laboratoire des Mycoplasnes, Institut Pasteur, 75724 Paris Cedex 15, Franice Received 2 August 1993/Accepted 17 December 1993 A fast and simple method to detect mycoplasmal contamination in simulated samples of animal sera by using a PCR was developed. The following five mycoplasma species that are major cell culture contaminants belonging to the class Mollicutes were investigated: Mycoplasma arginini, Acholeplasma laidlawii, Mycoplasma hyorhinis, Mycoplasma orale, and Mycoplasma fermentans. After a concentration step involving seeded sera, genus-specific primers were used to amplify a 717-bp DNA fragment within the 16S rRNA gene of mycoplasmas. In a second step, the universal PCR was followed by amplification of variable regions of the 16S rRNA gene by using species-specific primers, which allowed identification of contaminant mycoplasmas. With this method, 10 fg of purified DNA and 1 to 10 color-changing units of mycoplasmas could be detected. Since the sensitivity of the assay was increased 10-fold when the amplification products were hybridized with an internal mycoplasma-specific 32P-labelled oligonucleotide probe, a detection limit of 1 to 10 genome copies per PCR sample was obtained. This highly sensitive, specific, and simple assay may be a useful alternative to methods currently used to detect mycoplasmas in animal sera. Mycoplasmas (the trivial name for microorganisms belong- Like most cell cultures infected by mycoplasmas, serum infec- ing to the class Molliclutes) are the smallest self-replicating tions are rarely detected by visual inspection or light micros- bacteria.