Texto Completo
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Universidade Federal Do Rio Grande Do Sul Centro De Biotecnologia Programa De Pós-Graduação Em Biologia Celular E Molecular
UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL CENTRO DE BIOTECNOLOGIA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOLOGIA CELULAR E MOLECULAR Caracterização Molecular do Microbioma Hospitalar por Sequenciamento de Alto Desempenho Tese de Doutorado Pabulo Henrique Rampelotto Porto Alegre 2019 UNIVERSIDADE FEDERAL DO RIO GRANDE DO SUL CENTRO DE BIOTECNOLOGIA PROGRAMA DE PÓS-GRADUAÇÃO EM BIOLOGIA CELULAR E MOLECULAR Caracterização Molecular do Microbioma Hospitalar por Sequenciamento de Alto Desempenho Tese submetida ao Programa de Pós-Graduação em Biologia Celular e Molecular da UFRGS, como requisito parcial para a obtenção do grau de Doutor em Ciências Pabulo Henrique Rampelotto Orientador: Dr. Rogério Margis Porto Alegre, Abril de 2019 Instituições e fontes financiadoras: Instituições: Laboratório de Genomas e Populações de Plantas (LGPP), Departamento de Biofísica, UFRGS – Porto Alegre/RS, Brasil. Neoprospecta Microbiome Technologies SA – Florianópolis/SC, Brasil. Hospital Universitário Polydoro Ernani de São Thiago, Universidade Federal de Santa Catarina (UFSC) – Florianópolis/SC, Brasil. Fontes financiadoras: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil. Agradecimentos Aos meus familiares, pelo suporte incondicional em todos os momentos de minha vida. Ao meu orientador Prof. Rogério Margis, pela oportunidade e confiança. Aos colegas de laboratório, pelo apoio e amizade. Ao Programa de Pós-Graduação em Biologia Celular e Molecular, por todo o suporte. Aos inúmeros autores e co-autores que participaram dos meus diversos projetos editoriais, pelas brilhantes discussões em temas tão fascinantes. Enfim, a todos que, de alguma forma, contribuíram para a realização deste trabalho. “A tarefa não é tanto ver aquilo que ninguém viu, mas pensar o que ninguém ainda pensou sobre aquilo que todo mundo vê” (Arthur Schopenhauer) SUMÁRIO LISTA DE ABREVIATURAS .......................................................................................... -
MIB–MIP Is a Mycoplasma System That Captures and Cleaves Immunoglobulin G
MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G Yonathan Arfia,b,1, Laetitia Minderc,d, Carmelo Di Primoe,f,g, Aline Le Royh,i,j, Christine Ebelh,i,j, Laurent Coquetk, Stephane Claveroll, Sanjay Vasheem, Joerg Joresn,o, Alain Blancharda,b, and Pascal Sirand-Pugneta,b aINRA (Institut National de la Recherche Agronomique), UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; bUniversity of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; cInstitut Européen de Chimie et Biologie, UMS 3033, University of Bordeaux, 33607 Pessac, France; dInstitut Bergonié, SIRIC BRIO, 33076 Bordeaux, France; eINSERM U1212, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; fCNRS UMR 5320, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; gInstitut Européen de Chimie et Biologie, University of Bordeaux, 33607 Pessac, France; hInstitut de Biologie Structurale, University of Grenoble Alpes, F-38044 Grenoble, France; iCNRS, Institut de Biologie Structurale, F-38044 Grenoble, France; jCEA, Institut de Biologie Structurale, F-38044 Grenoble, France; kCNRS UMR 6270, Plateforme PISSARO, Institute for Research and Innovation in Biomedicine - Normandie Rouen, Normandie Université, F-76821 Mont-Saint-Aignan, France; lProteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076 Bordeaux Cedex, France; mJ. Craig Venter Institute, Rockville, MD 20850; nInternational Livestock Research Institute, 00100 Nairobi, Kenya; and oInstitute of Veterinary Bacteriology, University of Bern, CH-3001 Bern, Switzerland Edited by Roy Curtiss III, University of Florida, Gainesville, FL, and approved March 30, 2016 (received for review January 12, 2016) Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, introduced into naive herds (8). -
Genomic Islands in Mycoplasmas
G C A T T A C G G C A T genes Review Genomic Islands in Mycoplasmas Christine Citti * , Eric Baranowski * , Emilie Dordet-Frisoni, Marion Faucher and Laurent-Xavier Nouvel Interactions Hôtes-Agents Pathogènes (IHAP), Université de Toulouse, INRAE, ENVT, 31300 Toulouse, France; [email protected] (E.D.-F.); [email protected] (M.F.); [email protected] (L.-X.N.) * Correspondence: [email protected] (C.C.); [email protected] (E.B.) Received: 30 June 2020; Accepted: 20 July 2020; Published: 22 July 2020 Abstract: Bacteria of the Mycoplasma genus are characterized by the lack of a cell-wall, the use of UGA as tryptophan codon instead of a universal stop, and their simplified metabolic pathways. Most of these features are due to the small-size and limited-content of their genomes (580–1840 Kbp; 482–2050 CDS). Yet, the Mycoplasma genus encompasses over 200 species living in close contact with a wide range of animal hosts and man. These include pathogens, pathobionts, or commensals that have retained the full capacity to synthesize DNA, RNA, and all proteins required to sustain a parasitic life-style, with most being able to grow under laboratory conditions without host cells. Over the last 10 years, comparative genome analyses of multiple species and strains unveiled some of the dynamics of mycoplasma genomes. This review summarizes our current knowledge of genomic islands (GIs) found in mycoplasmas, with a focus on pathogenicity islands, integrative and conjugative elements (ICEs), and prophages. Here, we discuss how GIs contribute to the dynamics of mycoplasma genomes and how they participate in the evolution of these minimal organisms. -
Serological Evidence That Chlamydiae and Mycoplasmas Are Involved in Infertility of Women B
Serological evidence that chlamydiae and mycoplasmas are involved in infertility of women B. R. M\l=o/\ller,D. Taylor-Robinson, Patricia M. Furr, B. Toft and J. Allen Division of Sexually Transmitted Diseases, MRC Clinical Research Centre, Watford Road, Harrow, Middlesex HAI 3UJ, U.K., and ^Department of Obstetrics and Gynaecology, University of Aarhus, DK-8000, Aarhus, Denmark Summary. Women with a history of infertility for 2 or more years were examined by hysterosalpingography (HSG) and antibodies against Chlamydia trachomatis, Myco- plasma hominis and M. genitalium were measured by a microimmunofluorescence technique in sera obtained immediately before HSG. Of 45 women with abnormal HSG findings, 15 (33%) had antibodies to C. trachomatis and 16 (35\m=.\5%)to M. hominis. In contrast, of 61 women with normal HSG findings, only 8 (13%) and 7 (11\m=.\5%)had antibodies to these micro-organisms, respectively. Antibody against M. genitalium was found in 26 of the patients (20% abnormal HSG and 28% normal HSG), indicating the need for further investigation of the significance of this mycoplasma in female infertility. The present results do confirm, however, that C. trachomatis is an important cause of infertility in women and suggest strongly that M. hominis is implicated. Introduction Infertility in women is caused often by tubai damage after pelvic inflammatory disease. Chlamydia trachomatis is a well-known pathogen in upper genital-tract infections and accounts for 25-50% of all cases of pelvic inflammatory disease (Paavonen, 1979) while Mycoplasma hominis is believed to be responsible for about 25% of all the cases (Moller, 1983). -
MIAMI UNIVERSITY the Graduate School
MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Steven Lindau Distelhorst Candidate for the Degree Doctor of Philosophy ______________________________________ Dr. Mitchell F. Balish, Director ______________________________________ Kelly Z. Abshire, Reader ______________________________________ Natosha L. Finley, Reader ______________________________________ Joseph M. Carlin, Reader ______________________________________ Jack C. Vaughn, Graduate School Representative ABSTRACT UNDERSTANDING VIRULENCE FACTORS OF MYCOPLASMA PENETRANS: ATTACHMENT ORGANELLE ORGANIZATION AND GENE EXPRESSION by Steven Lindau Distelhorst The ability to establish and maintain cell polarity plays an important role in cellular organization for both functional and morphological integrity in eukaryotic and prokaryotic organisms. Like eukaryotes, bacteria, including the genomically reduced species of the Mycoplasma genus, use an array of cytoskeletal proteins to generate and maintain cellular polarity. Some mycoplasmas, such as Mycoplasma penetrans, exhibit a distinct polarized structure, known as the attachment organelle (AO), which is used for attachment to host cells and motility. The M. penetrans AO, like AOs of other mycoplasmas, contains a cytoskeletal structure at the core, but lacks any homologs of identified AO core proteins of other investigated mycoplasmas. To characterize the composition of the M. penetrans AO cytoskeleton we purified the detergent-insoluble core material and examined -
Mycoplasma Pneumoniae Terminal Organelle
MYCOPLASMA PNEUMONIAE TERMINAL ORGANELLE DEVELOPMENT AND GLIDING MOTILITY by BENJAMIN MICHAEL HASSELBRING (Under the Direction of Duncan Charles Krause) ABSTRACT With a minimal genome containing less than 700 open reading frames and a cell volume < 10% of that of model prokaryotes, Mycoplasma pneumoniae is considered among the smallest and simplest organisms capable of self-replication. And yet, this unique wall-less bacterium exhibits a remarkable level of cellular complexity with a dynamic cytoskeleton and a morphological asymmetry highlighted by a polar, membrane-bound terminal organelle containing an elaborate macromolecular core. The M. pneumoniae terminal organelle functions in distinct, and seemingly disparate cellular processes that include cytadherence, cell division, and presumably gliding motility, as individual cells translocate over surfaces with the cell pole harboring the structure engaged as the leading end. While recent years have witnessed a dramatic increase in the knowledge of protein interactions required for core stability and adhesin trafficking, the mechanism of M. pneumoniae gliding has not been defined nor have interdependencies between the various terminal organelle functions been assessed. The studies presented in the current volume describe the first genetic and molecular investigations into the location, components, architecture, and regulation of the M. pneumoniae gliding machinery. The data indicate that cytadherence and gliding motility are separable properties, and identify a subset of M. pneumoniae proteins contributing directly to the latter process. Characterizations of novel gliding-deficient mutants confirm that the terminal organelle contains the molecular gliding machinery, revealing that with the loss of a single terminal organelle cytoskeletal element, protein P41, terminal organelles detach from the cell body but retain gliding function. -
( 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 . -
Prevalence of Ureaplasma Urealyticum, Mycoplasma Hominis and Chlamydia Trachomatis in Patients with Uncomplicated Recurrent Urin
Nephrology and Renal Diseases Research Article ISSN: 2399-908X Prevalence of Ureaplasma urealyticum, Mycoplasma hominis and Chlamydia trachomatis in patients with uncomplicated recurrent urinary tract infections Jadranka Vlasic-Matas1*, Hrvoje Raos2, Marijana Vuckovic2, Stjepan Radic2 and Vesna Capkun3 1Polyclinic Nephrology Department, Split, Croatia 2School of Medicine, University of Split, Split, Croatia 3Department of Nuclear Medicine, Split University Hospital Center, Split, Croatia Abstract Aim: To assess the prevalence of Ureaplasma urealyticum, Mycoplasma hominis and Chlamydia trachomatis in patients with chronic urinary tract infections (UTIs) and its correlation with leukocyturia and symptoms. Methods: The study included 220 patients (130 women and 90 men) presenting with chronic voiding symptoms and sterile leukocyturia. Urine, urethral swabs and cervical swabs (for women patients) were taken to determine the presence of these pathogens. Patients were treated by tetracycline and followed up three and six months after initial therapy. Results: In 186 (85%) out of 220 patients, U. urealyticum was found, while C. trachomatis was present in 34 patients (15%). In majority of female patients (112 out of 130; 86%) U. urealyticum was found. In addition to ureaplasma, in eight patients M. hominis was found. C. trachomatis was identified in 18 female patients (14%). In 74 out of 90 (82%) male patients U. urealyticum was detected while in six of them M. hominis was also found. C. trachomatis was identified in 16 male patients (18%). U. urealyticum was significantly related to leukocyturia, as opposed to C. trachomatis (p<0,001). Women had more frequent symptomatology (p = 0,015) and higer leukocyturia (p<0.001). Conclusion: Leukocyturia is more common find in U. -
International Journal of Systematic and Evolutionary Microbiology
International Journal of Systematic and Evolutionary Microbiology Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus --Manuscript Draft-- Manuscript Number: IJSEM-D-17-00095R1 Full Title: Mycoplasma tullyi sp. nov., isolated from penguins of the genus Spheniscus Article Type: Note Section/Category: New taxa - other bacteria Keywords: Mollicutes Mycoplasma sp. nov. penguin Spheniscus humboldti Corresponding Author: Ana S. Ramirez, Ph.D. Universidad de Las Palmas de Garn Canaria Arucas, Las Palmas SPAIN First Author: Christine A. Yavari, PhD Order of Authors: Christine A. Yavari, PhD Ana S. Ramirez, Ph.D. Robin A. J. Nicholas, PhD Alan D. Radford, PhD Alistair C. Darby, PhD Janet M. Bradbury, PhD Manuscript Region of Origin: UNITED KINGDOM Abstract: A mycoplasma isolated from the liver of a dead Humboldt penguin (Spheniscus humboldti) and designated strain 56A97, was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism was most closely related to M. gallisepticum and M. imitans (99.7 and 99.9% similarity, respectively). The average DNA-DNA hybridization (DDH) values between strain 56A97 and M. gallisepticum and M. imitans were 39.5% and 30%, respectively and the values for Genome-to Genome Distance Calculator (GGDC) gave a result of 29.10 and 23.50% respectively. The 16S-23S rRNA intergenic spacer was 72-73% similar to M. gallisepticum strains and 52.2% to M. imitans. A partial sequence of rpoB was 91.1- 92% similar to M. gallisepticum strains and 84.7 % to M. imitans. Colonies possessed a typical fried-egg appearance and electron micrographs revealed the lack of a cell wall and a nearly-spherical morphology, with an electron dense tip-like structure on some flask-shaped cells. -
Examining the Link Between Macrophyte Diversity, Bacterial
EXAMINING THE LINK BETWEEN MACROPHYTE DIVERSITY, BACTERIAL DIVERSITY, AND DENITRIFICATION FUNCTION IN WETLANDS DISSERTATION Presented in Partial Fulfillment of the Requirements for The Degree of Doctor of Philosophy in the Graduate School of The Ohio State University By Janice M. Gilbert, B.E.S., B.Ed., M.E.S., M.S. ***** The Ohio State University 2004 Dissertation Committee: Professor Virginie Bouchard, Adviser Approved by Professor Serita D. Frey, Co-adviser Professor Olli H. Tuovinen Professor Frederick C. Michel, Jr. Adviser Environmental Science Graduate Program ABSTRACT The relationship between aquatic plant (macrophyte) diversity, bacterial diversity, and the biochemical reduction of nitrate (denitrification) within wetlands was examined. Denitrification occurs under anoxic conditions when nitrate is reduced to either nitrous oxide (N2O), or dinitrogen (N2). Although previous studies have identified physical and chemical factors regulating the production of either gas in wetlands, the role that macrophyte diversity plays in this process is not known. The central hypothesis, based on the niche-complimentarity mechanism, was that an increase in macrophyte diversity would lead to increased bacterial diversity, increased denitrification, and decreased N2O flux. This hypothesis was investigated in two mesocosm studies to control environmental conditions while altering macrophyte functional groups (FG) and functional group diversity. In Study #1, five macrophyte functional groups (clonal dominants, tussocks, reeds, facultative annuals, and obligate annuals) were each represented by two species. Fifty-five mesocosms with 5-6 replicates of 0, 1, 2, 3, 4, or 5 macrophyte FG (0-10 species) were established in the spring of 2001 and sampled in August 2001, September 2001, and April 2002. -
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. -
The Variable Internal Structure of the Mycoplasma Penetrans
RESEARCH ARTICLE crossm The Variable Internal Structure of the Downloaded from Mycoplasma penetrans Attachment Organelle Revealed by Biochemical and Microscopic Analyses: Implications for Attachment Organelle Mechanism and http://jb.asm.org/ Evolution Steven L. Distelhorst,a Dominika A. Jurkovic,a* Jian Shi,b* Grant J. Jensen,b,c Mitchell F. Balisha Department of Microbiology, Miami University, Oxford, Ohio, USAa; Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California, USAb; Howard Hughes Medical Institute, California on June 2, 2017 by CALIFORNIA INSTITUTE OF TECHNOLOGY Institute of Technology, Pasadena, California, USAc ABSTRACT Although mycoplasmas have small genomes, many of them, including Received 1 February 2017 Accepted 27 the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment March 2017 organelle (AO) that is used for both adherence to host cells and gliding motility. Accepted manuscript posted online 3 April However, the irregular phylogenetic distribution of similar structures within the my- 2017 coplasmas, as well as compositional and ultrastructural differences among these AOs, Citation Distelhorst SL, Jurkovic DA, Shi J, Jensen GJ, Balish MF. 2017. The variable suggests that AOs have arisen several times through convergent evolution. We in- internal structure of the Mycoplasma penetrans vestigated the ultrastructure and protein composition of the cytoskeleton-like mate- attachment organelle revealed by biochemical and microscopic analyses: implications for rial of the M. penetrans AO with several forms of microscopy and biochemical analy- attachment organelle mechanism and sis, to determine whether the M. penetrans AO was constructed at the molecular evolution. J Bacteriol 199:e00069-17. https:// level on principles similar to those of other mycoplasmas, such as Mycoplasma pneu- doi.org/10.1128/JB.00069-17.