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Structural and Functional Characterization of the Fimh Adhesin of Uropathogenic Escherichia Coli and Its Novel Applications
Open Access Journal of Bacteriology and Mycology Research Article Structural and Functional Characterization of the FimH Adhesin of Uropathogenic Escherichia coli and Its Novel Applications Neamati F1, Moniri R2*, Khorshidi A1 and Saffari M1 Abstract 1Department of Microbiology and Immunology, School Type 1 fimbriae are responsible for bacterial pathogenicity and biofilm of Medicine, Kashan University of Medical Sciences, production, which are important virulence factors in uropathogenic Escherichia Kashan, Iran coli strains. Many articles are published on FimH, but each examined a specific 2Department of Microbiology, Faculty of Medicine, aspect of this protein. The current review study aimed at focusing on structure Kashan University of Medical Sciences, Qutb Ravandi and conformational changes and describing efforts to use this protein in novel Boulevard, Kashan, Iran potential treatments for urinary tract infections, typing methods, and expression *Corresponding author: Moniri R, Department of systems. The current study was the first review that briefly and effectively Microbiology, Faculty of Medicine, Kashan University of examined issues related to FimH adhesin. Medical Sciences, Qutb Ravandi Boulevard, Kashan, Iran Keywords: Uropathogenic E. coli; FimH Adhesion; FimH Typing; Received: June 05, 2020; Accepted: July 03, 2020; Conformation Switch; FimH Antagonists Published: July 10, 2020 Abbreviations FimH proteins play important roles in UPEC pathogenicity and the formation of bacterial biofilms [7]. FimH binds to mannosylated UTIs: Urinary Tract Infections; UPEC: Uropathogenic E. uroplakin proteins in the bladder lumen and invades into the Coli; IBCs: Intracellular Bacterial Communities; QIR: Quiescent superficial umbrella cells [8]. After the invasion, UPEC is expelled out Intracellular Reservoir; LD: Mannose-Binding Lectin; PD: Fimbria- of the cell in a TLR4 dependent process, or escape into the cytoplasm Incorporating Pilin; MBP: Mannose-Binding Pocket; LIBS: Ligand- [9]. -
Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
Catalogue of Bacteria Shapes
We first tried to use the most general shape associated with each genus, which are often consistent across species (spp.) (first choice for shape). If there was documented species variability, either the most common species (second choice for shape) or well known species (third choice for shape) is shown. Corynebacterium: pleomorphic bacilli. Due to their snapping type of division, cells often lie in clusters resembling chinese letters (https://microbewiki.kenyon.edu/index.php/Corynebacterium) Shown is Corynebacterium diphtheriae Figure 1. Stained Corynebacterium cells. The "barred" appearance is due to the presence of polyphosphate inclusions called metachromatic granules. Note also the characteristic "Chinese-letter" arrangement of cells. (http:// textbookofbacteriology.net/diphtheria.html) Lactobacillus: Lactobacilli are rod-shaped, Gram-positive, fermentative, organotrophs. They are usually straight, although they can form spiral or coccobacillary forms under certain conditions. (https://microbewiki.kenyon.edu/index.php/ Lactobacillus) Porphyromonas: A genus of small anaerobic gram-negative nonmotile cocci and usually short rods thatproduce smooth, gray to black pigmented colonies the size of which varies with the species. (http:// medical-dictionary.thefreedictionary.com/Porphyromonas) Shown: Porphyromonas gingivalis Moraxella: Moraxella is a genus of Gram-negative bacteria in the Moraxellaceae family. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli or, as in the case of Moraxella catarrhalis, diplococci in morphology (https://en.wikipedia.org/wiki/Moraxella). *This one could be changed to a diplococcus shape because of moraxella catarrhalis, but i think the short rods are fair given the number of other moraxella with them. Jeotgalicoccus: Jeotgalicoccus is a genus of Gram-positive, facultatively anaerobic, and halotolerant to halophilicbacteria. -
Identification of Type 3 Fimbriae in Uropathogenic Escherichia Coli
JOURNAL OF BACTERIOLOGY, Feb. 2008, p. 1054–1063 Vol. 190, No. 3 0021-9193/08/$08.00ϩ0 doi:10.1128/JB.01523-07 Copyright © 2008, American Society for Microbiology. All Rights Reserved. Identification of Type 3 Fimbriae in Uropathogenic Escherichia coli Reveals a Role in Biofilm Formationᰔ Cheryl-Lynn Y. Ong,1 Glen C. Ulett,1 Amanda N. Mabbett,1 Scott A. Beatson,1 Richard I. Webb,2 Wayne Monaghan,3 Graeme R. Nimmo,3 David F. Looke,4 1 1 Alastair G. McEwan, and Mark A. Schembri * Downloaded from School of Molecular and Microbial Sciences1 and Centre for Microscopy and Microanalysis,2 University of Queensland, Brisbane, Australia, and Queensland Health Pathology Service3 and Infection Management Services, Princess Alexandra Hospital, Brisbane, Australia4 Received 21 September 2007/Accepted 17 November 2007 Catheter-associated urinary tract infection (CAUTI) is the most common nosocomial infection in the United States. Uropathogenic Escherichia coli (UPEC), the most common cause of CAUTI, can form biofilms on indwelling catheters. Here, we identify and characterize novel factors that affect biofilm formation by UPEC http://jb.asm.org/ strains that cause CAUTI. Sixty-five CAUTI UPEC isolates were characterized for phenotypic markers of urovirulence, including agglutination and biofilm formation. One isolate, E. coli MS2027, was uniquely proficient at biofilm growth despite the absence of adhesins known to promote this phenotype. Mini-Tn5 mutagenesis of E. coli MS2027 identified several mutants with altered biofilm growth. Mutants containing insertions in genes involved in O antigen synthesis (rmlC and manB) and capsule synthesis (kpsM) possessed enhanced biofilm phenotypes. Three independent mutants deficient in biofilm growth contained an insertion in a gene locus homologous to the type 3 chaperone-usher class fimbrial genes of Klebsiella pneumoniae. -
Porphyromonas Gingivalis, Strain F0566 Catalog
Product Information Sheet for HM-1141 Porphyromonas gingivalis, Strain F0566 immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze- thaw cycles should be avoided. Catalog No. HM-1141 Growth Conditions: For research use only. Not for human use. Media: Supplemented Tryptic Soy broth or equivalent Contributor: Tryptic Soy agar with 5% defibrinated sheep blood or Floyd E. Dewhirst, D.D.S., Ph.D., Senior Member of the Staff, Supplemented Tryptic Soy agar or equivalent Department of Microbiology and Jacques Izard, Assistant Incubation: Member of the Staff, Department of Molecular Genetics, The Temperature: 37°C Forsyth Institute, Cambridge, Massachusetts, USA Atmosphere: Anaerobic Propagation: Manufacturer: 1. Keep vial frozen until ready for use, then thaw. BEI Resources 2. Transfer the entire thawed aliquot into a single tube of broth. Product Description: 3. Use several drops of the suspension to inoculate an Bacteria Classification: Porphyromonadaceae, agar slant and/or plate. Porphyromonas 4. Incubate the tube, slant and/or plate at 37°C for 24 to Species: Porphyromonas gingivalis 72 hours. Broth cultures should include shaking. Strain: F0566 Original Source: Porphyromonas gingivalis (P. gingivalis), Citation: strain F0566 was isolated in October 1987 from the tooth Acknowledgment for publications should read “The following of a patient diagnosed with moderate periodontitis in the reagent was obtained through BEI Resources, NIAID, NIH as United States.1 part of the Human Microbiome Project: Porphyromonas Comments: P. gingivalis, strain F0566 (HMP ID 1989) is a gingivalis, Strain F0566, HM-1141.” reference genome for The Human Microbiome Project (HMP). HMP is an initiative to identify and characterize Biosafety Level: 2 human microbial flora. -
Introduction to Bacteriology and Bacterial Structure/Function
INTRODUCTION TO BACTERIOLOGY AND BACTERIAL STRUCTURE/FUNCTION LEARNING OBJECTIVES To describe historical landmarks of medical microbiology To describe Koch’s Postulates To describe the characteristic structures and chemical nature of cellular constituents that distinguish eukaryotic and prokaryotic cells To describe chemical, structural, and functional components of the bacterial cytoplasmic and outer membranes, cell wall and surface appendages To name the general structures, and polymers that make up bacterial cell walls To explain the differences between gram negative and gram positive cells To describe the chemical composition, function and serological classification as H antigen of bacterial flagella and how they differ from flagella of eucaryotic cells To describe the chemical composition and function of pili To explain the unique chemical composition of bacterial spores To list medically relevant bacteria that form spores To explain the function of spores in terms of chemical and heat resistance To describe characteristics of different types of membrane transport To describe the exact cellular location and serological classification as O antigen of Lipopolysaccharide (LPS) To explain how the structure of LPS confers antigenic specificity and toxicity To describe the exact cellular location of Lipid A To explain the term endotoxin in terms of its chemical composition and location in bacterial cells INTRODUCTION TO BACTERIOLOGY 1. Two main threads in the history of bacteriology: 1) the natural history of bacteria and 2) the contagious nature of infectious diseases, were united in the latter half of the 19th century. During that period many of the bacteria that cause human disease were identified and characterized. 2. Individual bacteria were first observed microscopically by Antony van Leeuwenhoek at the end of the 17th century. -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
A Double, Long Polar Fimbria Mutant of Escherichia Coli O157:H7 Expresses Curli and Exhibits Reduced in Vivo Colonization
A Double, Long Polar Fimbria Mutant of Escherichia coli O157:H7 Expresses Curli and Exhibits Reduced in Vivo Colonization The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Lloyd, Sonja J., Jennifer M. Ritchie, Maricarmen Rojas-Lopez, Carla A. Blumentritt, Vsevolod L. Popov, Jennifer L. Greenwich, Matthew K. Waldor, and Alfredo G. Torres. 2012. “A Double, Long Polar Fimbria Mutant of Escherichia Coli O157:H7 Expresses Curli and Exhibits ReducedIn VivoColonization.” Edited by S. M. Payne. Infection and Immunity 80 (3): 914–20. https://doi.org/10.1128/ iai.05945-11. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:41483527 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA A Double, Long Polar Fimbria Mutant of Escherichia coli O157:H7 Expresses Curli and Exhibits Reduced In Vivo Colonization Sonja J. Lloyd,a Jennifer M. Ritchie,d* Maricarmen Rojas-Lopez,a Carla A. Blumentritt,a Vsevolod L. Popov,b Jennifer L. Greenwich,d Matthew K. Waldor,d and Alfredo G. Torresa,b,c Departments of Microbiology and Immunologya and Pathologyb and Sealy Center for Vaccine Development,c University of Texas Medical Branch, Galveston, Texas, USA, and Channing Laboratory, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USAd Escherichia coli O157:H7 causes food and waterborne enteric infections that can result in hemorrhagic colitis and life- threatening hemolytic uremic syndrome. -
Origin and Evolution of Eukaryotic Compartmentalization
TESI DOCTORAL UPF 2016 Origin and evolution of eukaryotic compartmentalization Alexandros Pittis Director Dr. Toni Gabaldon´ Comparative Genomics Group Bioinformatics and Genomics Department Centre for Genomic Regulation (CRG) To my father Stavros for the PhD he never did Acknowledgments Looking back at the years of my PhD in the Comparative Genomics group at CRG, I feel it was equally a process of scientific, as well as personal development. All this time I was very privileged to be surrounded by people that offered me their generous support in both fronts. And they were available in the very moments that I was fighting more myself than the unsolvable (anyway) comparative genomics puzzles. I hope that in the future I will have many times the chance to express them my appreciation, way beyond these few words. First, to Toni, my supervisor, for all his support, and patience, and confidence, and respect, especially at the moments that things did not seem that promising. He offered me freedom, to try, to think, to fail, to learn, to achieve that few enjoy during their PhD, and I am very thankful to him. Then, to my good friends and colleagues, those that I found in the group already, and others that joined after me. A very special thanks to Marinita and Jaime, for all their valuable time, and guidance and paradigm, which nevertheless I never managed to follow. They have both marked my phylogenomics path so far and I cannot escape. To Les and Salvi, my fellow students and pals at the time for all that we shared; to Gab and Fran and Dam, for -
Correlation of the Lung Microbiota with Metabolic Profiles in Bronchoalveolar Lavage Fluid in HIV Infection Sushma K
Cribbs et al. Microbiome (2016) 4:3 DOI 10.1186/s40168-016-0147-4 RESEARCH Open Access Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection Sushma K. Cribbs1,2*, Karan Uppal2, Shuzhao Li2, Dean P. Jones2, Laurence Huang3, Laura Tipton4,5, Adam Fitch6, Ruth M. Greenblatt7, Lawrence Kingsley8, David M. Guidot1,2, Elodie Ghedin5 and Alison Morris6 Abstract Background: While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung’s bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients. Results: Targeted sequencing of the 16S rRNA gene was used to analyze the bacterial community structure and liquid chromatography-high-resolution mass spectrometry was used to detect features in bronchoalveolar lavage fluid. Global integration of all metabolic features with microbial species was done using sparse partial least squares regression. Thirty-nine HIV-infected subjects and 20 HIV-uninfected controls without acute respiratory symptoms were enrolled. Twelve mass-to-charge ratio (m/z) features from C18 analysis were significantly different between HIV-infected individuals and controls (false discovery rate (FDR) = 0.2); another 79 features were identified by network analysis. Further metabolite analysis demonstrated that four features were significantly overrepresented in the bronchoalveolar lavage (BAL) fluid of HIV-infected individuals compared to HIV-uninfected, including cystine, two complex carbohydrates, and 3,5-dibromo-L-tyrosine. -
The Protozoan Nucleus. Molecular and Biochemical Parasitology, 209(1-2), Pp
McCulloch, R., and Navarro, M. (2016) The protozoan nucleus. Molecular and Biochemical Parasitology, 209(1-2), pp. 76-87. (doi:10.1016/j.molbiopara.2016.05.002) This is the author’s final accepted version. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/135296/ Deposited on: 22 February 2017 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk *Manuscript Click here to view linked References The protozoan nucleus Richard McCulloch1 and Miguel Navarro2 1. The Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davis Building, 120 University Place, Glasgow, G12 8TA, U.K. Telephone: 01413305946 Fax: 01413305422 Email: [email protected] 2. Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (CSIC), Avda. del Conocimiento s/n, 18100 Granada, Spain. Email: [email protected] Correspondence can be sent to either of above authors Keywords: nucleus; mitosis; nuclear envelope; chromosome; DNA replication; gene expression; nucleolus; expression site body 1 Abstract The nucleus is arguably the defining characteristic of eukaryotes, distinguishing their cell organisation from both bacteria and archaea. Though the evolutionary history of the nucleus remains the subject of debate, its emergence differs from several other eukaryotic organelles in that it appears not to have evolved through symbiosis, but by cell membrane elaboration from an archaeal ancestor. Evolution of the nucleus has been accompanied by elaboration of nuclear structures that are intimately linked with most aspects of nuclear genome function, including chromosome organisation, DNA maintenance, replication and segregation, and gene expression controls. -
S41598-018-20067-Z.Pdf
www.nature.com/scientificreports OPEN Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fmbria Received: 11 May 2017 Accepted: 12 January 2018 from the periodontal pathogen Published: xx xx xxxx Porphyromonas gingivalis Michael Hall1, Yoshiaki Hasegawa2, Fuminobu Yoshimura2 & Karina Persson1 Very little is known about how fmbriae of Bacteroidetes bacteria are assembled. To shed more light on this process, we solved the crystal structures of the shaft protein Mfa1, the regulatory protein Mfa2, and the tip protein Mfa3 from the periodontal pathogen Porphyromonas gingivalis. Together these build up part of the Mfa1 fmbria and represent three of the fve proteins, Mfa1-5, encoded by the mfa1 gene cluster. Mfa1, Mfa2 and Mfa3 have the same overall fold i.e., two β-sandwich domains. Upon polymerization, the frst β-strand of the shaft or tip protein is removed by indigenous proteases. Although the resulting void is expected to be flled by a donor-strand from another fmbrial protein, the mechanism by which it does so is still not established. In contrast, the frst β-strand in Mfa2, the anchoring protein, is frmly attached by a disulphide bond and is not cleaved. Based on the structural information, we created multiple mutations in P. gingivalis and analysed their efect on fmbrial polymerization and assembly in vivo. Collectively, these data suggest an important role for the C-terminal tail of Mfa1, but not of Mfa3, afecting both polymerization and maturation of downstream fmbrial proteins. Humans co-exist with microorganisms that play signifcant roles in our biology. Te largest bacterial population is found in the gut, where species of Bacteroidetes are the most common Gram-negative anaerobes1.