Evolutionary Dynamics of the Vapd Gene in Helicobacter Pylori and Its
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Structural Characterization of Helicobacter Pylori Proteins Contributing to Stomach Colonization
Università degli Studi di Padova Dipartimento di Biologia Scuola di Dottorato di Ricerca in Bioscienze e Biotecnologie Indirizzo: Biotecnologie Ciclo XXVIII STRUCTURAL CHARACTERIZATION OF HELICOBACTER PYLORI PROTEINS CONTRIBUTING TO STOMACH COLONIZATION Direttore della Scuola: Ch.mo Prof. Paolo Bernardi Coordinatore di Indirizzo: Ch.ma Prof.ssa Fiorella Lo Schiavo Supervisore: Ch.mo Prof. Giuseppe Zanotti Dottorando: Maria Elena Compostella 31 Gennaio 2016 Università degli Studi di Padova Department of Biology School of Biosciences and Biotechnology Curriculum: Biotechnology XXVIII Cycle STRUCTURAL CHARACTERIZATION OF HELICOBACTER PYLORI PROTEINS CONTRIBUTING TO STOMACH COLONIZATION Director of the Ph.D. School: Ch.mo Prof. Paolo Bernardi Coordinator of the Curriculum: Ch.ma Prof.ssa Fiorella Lo Schiavo Supervisor: Ch.mo Prof. Giuseppe Zanotti Ph.D. Candidate: Maria Elena Compostella 31 January 2016 Contents ABBREVIATIONS AND SYMBOLS IV SUMMARY 9 SOMMARIO 15 1. INTRODUCTION 21 1.1 HELICOBACTER PYLORI 23 1.2 GENETIC VARIABILITY 26 1.2.1 GENOME COMPARISON 26 1.2.1.1 HELICOBACTER PYLORI 26695 26 1.2.1.2 HELICOBACTER PYLORI J99 28 1.2.2 CORE GENOME 30 1.2.3 MECHANISMS GENERATING GENETIC VARIABILITY 31 1.2.3.1 MUTAGENESIS 32 1.2.3.2 RECOMBINATION 35 1.2.4 HELICOBACTER PYLORI AS A “QUASI SPECIES” 37 1.2.5 CLASSIFICATION OF HELICOBACTER PYLORI STRAINS 38 1.3 EPIDEMIOLOGY 40 1.3.1 INCIDENCE AND PREVALENCE OF HELICOBACTER PYLORI INFECTION 40 1.3.2 SOURCE AND TRANSMISSION 42 1.4 ADAPTATION AND GASTRIC COLONIZATION 47 1.4.1 ACID ADAPTATION 49 1.4.2 MOTILITY AND CHEMIOTAXIS 60 1.4.3 ADHESION 65 1.5 PATHOGENESIS AND VIRULENCE FACTORS 72 1.5.1 VACUOLATING CYTOTOXIN A 78 1.5.2 CAG PATHOGENICITY ISLAND AND CYTOTOXIN-ASSOCIATED GENE A 83 1.5.3 NEUTROPHIL-ACTIVATING PROTEIN 90 1.6 HELICOBACTER PYLORI AND GASTRODUODENAL DISEASES 92 1.7 ERADICATION AND POTENTIAL BENEFITS 97 2. -
Food Or Beverage Product, Or Probiotic Composition, Comprising Lactobacillus Johnsonii 456
(19) TZZ¥¥¥ _T (11) EP 3 536 328 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 11.09.2019 Bulletin 2019/37 A61K 35/74 (2015.01) A61K 35/66 (2015.01) A61P 35/00 (2006.01) (21) Application number: 19165418.5 (22) Date of filing: 19.02.2014 (84) Designated Contracting States: • SCHIESTL, Robert, H. AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Encino, CA California 91436 (US) GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO • RELIENE, Ramune PL PT RO RS SE SI SK SM TR Los Angeles, CA California 90024 (US) • BORNEMAN, James (30) Priority: 22.02.2013 US 201361956186 P Riverside, CA California 92506 (US) 26.11.2013 US 201361909242 P • PRESLEY, Laura, L. Santa Maria, CA California 93458 (US) (62) Document number(s) of the earlier application(s) in • BRAUN, Jonathan accordance with Art. 76 EPC: Tarzana, CA California 91356 (US) 14753847.4 / 2 958 575 (74) Representative: Müller-Boré & Partner (71) Applicant: The Regents of the University of Patentanwälte PartG mbB California Friedenheimer Brücke 21 Oakland, CA 94607 (US) 80639 München (DE) (72) Inventors: Remarks: • YAMAMOTO, Mitsuko, L. This application was filed on 27-03-2019 as a Alameda, CA California 94502 (US) divisional application to the application mentioned under INID code 62. (54) FOOD OR BEVERAGE PRODUCT, OR PROBIOTIC COMPOSITION, COMPRISING LACTOBACILLUS JOHNSONII 456 (57) The present invention relates to food products, beverage products and probiotic compositions comprising Lacto- bacillus johnsonii 456. EP 3 536 328 A1 Printed by Jouve, 75001 PARIS (FR) EP 3 536 328 A1 Description CROSS-REFERENCE TO RELATED APPLICATIONS 5 [0001] This application claims the benefit of U.S. -
In Silico Evolutionary Analysis of Helicobacter Pylori Outer Membrane Phospholipase a (OMPLA) Hilde S Vollan1*, Tone Tannæs1, Yoshio Yamaoka2 and Geir Bukholm3,4
Vollan et al. BMC Microbiology 2012, 12:206 http://www.biomedcentral.com/1471-2180/12/206 RESEARCH ARTICLE Open Access In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA) Hilde S Vollan1*, Tone Tannæs1, Yoshio Yamaoka2 and Geir Bukholm3,4 Abstract Background: In the past decade, researchers have proposed that the pldA gene for outer membrane phospholipase A (OMPLA) is important for bacterial colonization of the human gastric ventricle. Several conserved Helicobacter pylori genes have distinct genotypes in different parts of the world, biogeographic patterns that can be analyzed through phylogenetic trees. The current study will shed light on the importance of the pldA gene in H. pylori. In silico sequence analysis will be used to investigate whether the bacteria are in the process of preserving, optimizing, or rejecting the pldA gene. The pldA gene will be phylogenetically compared to other housekeeping (HK) genes, and a possible origin via horizontal gene transfer (HGT) will be evaluated through both intra- and inter- species evolutionary analyses. Results: In this study, pldA gene sequences were phylogenetically analyzed and compared with a large reference set of concatenated HK gene sequences. A total of 246 pldA nucleotide sequences were used; 207 were from Norwegian isolates, 20 were from Korean isolates, and 19 were from the NCBI database. Best-fit evolutionary models were determined with MEGA5 ModelTest for the pldA (K80 + I + G) and HK (GTR + I + G) sequences, and maximum likelihood trees were constructed. Both HK and pldA genes showed biogeographic clustering. Horizontal gene transfer was inferred based on significantly different GC contents, the codon adaptation index, and a phylogenetic conflict between a tree of OMPLA protein sequences representing 171 species and a tree of the AtpA HK protein for 169 species. -
Upper and Lower Case Letters to Be Used
Isolation, characterization and genome sequencing of a soil-borne Citrobacter freundii strain capable of detoxifying trichothecene mycotoxins by Rafiqul Islam A Thesis Presented to The University of Guelph In Partial Fulfilment of Requirements for the Degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Rafiqul Islam, April, 2012 ABSTRACT ISOLATION, CHARACTERIZATION AND GENOME SEQUENCING OF A SOIL- BORNE CITROBACTER FREUNDII STRAIN CAPABLE OF DETOXIFIYING TRICHOTHECENE MYCOTOXINS Rafiqul Islam Advisors: University of Guelph, 2012 Dr. K. Peter Pauls Dr. Ting Zhou Cereals are frequently contaminated with tricthothecene mycotoxins, like deoxynivalenol (DON, vomitoxin), which are toxic to humans, animals and plants. The goals of the research were to discover and characterize microbes capable of detoxifying DON under aerobic conditions and moderate temperatures. To identify microbes capable of detoxifying DON, five soil samples collected from Southern Ontario crop fields were tested for the ability to convert DON to a de-epoxidized derivative. One soil sample showed DON de-epoxidation activity under aerobic conditions at 22-24°C. To isolate the microbes responsible for DON detoxification (de-epoxidation) activity, the mixed culture was grown with antibiotics at 50ºC for 1.5 h and high concentrations of DON. The treatments resulted in the isolation of a pure DON de-epoxidating bacterial strain, ADS47, and phenotypic and molecular analyses identified the bacterium as Citrobacter freundii. The bacterium was also able to de-epoxidize and/or de-acetylate 10 other food-contaminating trichothecene mycotoxins. A fosmid genomic DNA library of strain ADS47 was prepared in E. coli and screened for DON detoxification activity. However, no library clone was found with DON detoxification activity. -
Genomics of Helicobacter Species 91
Genomics of Helicobacter Species 91 6 Genomics of Helicobacter Species Zhongming Ge and David B. Schauer Summary Helicobacter pylori was the first bacterial species to have the genome of two independent strains completely sequenced. Infection with this pathogen, which may be the most frequent bacterial infec- tion of humanity, causes peptic ulcer disease and gastric cancer. Other Helicobacter species are emerging as causes of infection, inflammation, and cancer in the intestine, liver, and biliary tract, although the true prevalence of these enterohepatic Helicobacter species in humans is not yet known. The murine pathogen Helicobacter hepaticus was the first enterohepatic Helicobacter species to have its genome completely sequenced. Here, we consider functional genomics of the genus Helico- bacter, the comparative genomics of the genus Helicobacter, and the related genera Campylobacter and Wolinella. Key Words: Cytotoxin-associated gene; H-Proteobacteria; gastric cancer; genomic evolution; genomic island; hepatobiliary; peptic ulcer disease; type IV secretion system. 1. Introduction The genus Helicobacter belongs to the family Helicobacteriaceae, order Campylo- bacterales, and class H-Proteobacteria, which is also known as the H subdivision of the phylum Proteobacteria. The H-Proteobacteria comprise of a relatively small and recently recognized line of descent within this extremely large and phenotypically diverse phy- lum. Other genera that colonize and/or infect humans and animals include Campylobac- ter, Arcobacter, and Wolinella. These organisms are all microaerophilic, chemoorgano- trophic, nonsaccharolytic, spiral shaped or curved, and motile with a corkscrew-like motion by means of polar flagella. Increasingly, free living H-Proteobacteria are being recognized in a wide range of environmental niches, including seawater, marine sedi- ments, deep-sea hydrothermal vents, and even as symbionts of shrimp and tubeworms in these environments. -
The Serology of Citrobacter Koseri, Levinea Malonatica, and Levinea Amalonatica
THE SEROLOGY OF CITROBACTER KOSERI, LEVINEA MALONATICA, AND LEVINEA AMALONATICA R. J. GROSSAND B. ROWE Salmonella and Shigella Reference Laboratory, Central Public Health Laboratory, Colindale Avenue, London NW9 SHT FREDERIKSEN(1970) described a collection of 30 strains belonging to the genus Citrobacter, but differing in several respects from C.freundii. Adonitol was fermented, malonate was utilised, indole was produced, and there was no growth in Moeller’s potassium cyanide medium (KCN). Hydrogen sulphide (H2S) production in ferric chloride gelatin was weak. Frederiksen considered that these strains should be regarded as a new species, and proposed the name C. koseri. Booth and McDonald (1971) examined 40 biochemically similar strains and proposed that they be regarded as a new species of Citrobacter. Young et al. (1971) studied 108 strains and proposed the establishment of a new genus, Levinea, having two species, L. malonatica and L. amalonatica. The biochemical reactions described for L. malonatica were similar to those of C. koseri, but H2S production was not detected in triple sugar iron agar (TSI agar). The reactions of L. amalonatica differed in that adonitol was not fermented, malonate was not utilised, and growth was always seen in KCN. Limited serological studies showed considerable antigenic sharing within the proposed species L. malonatica. Gross, Rowe and Easton (1973) studied four cases of neonatal meningitis in a premature-baby unit; C. koseri was the causative organism in all, but serological studies showed that two distinct serotypes were involved. We now report a biochemical and serological study of representative strains from all these authors, and a previously undescribed strain. -
Biofilm Formation by Pathogens Causing Ventilator-Associated Pneumonia at Intensive Care Units in a Tertiary Care Hospital: an Armor for Refuge
Hindawi BioMed Research International Volume 2021, Article ID 8817700, 10 pages https://doi.org/10.1155/2021/8817700 Research Article Biofilm Formation by Pathogens Causing Ventilator-Associated Pneumonia at Intensive Care Units in a Tertiary Care Hospital: An Armor for Refuge Sujata Baidya ,1 Sangita Sharma,1 Shyam Kumar Mishra ,1,2 Hari Prasad Kattel,1 Keshab Parajuli,1 and Jeevan Bahadur Sherchand1 1Department of Clinical Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal 2School of Optometry and Vision Science, University of New South Wales, Australia Correspondence should be addressed to Sujata Baidya; [email protected] Received 11 September 2020; Revised 26 January 2021; Accepted 21 May 2021; Published 29 May 2021 Academic Editor: Stanley Brul Copyright © 2021 Sujata Baidya et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. Emerging threat of drug resistance among pathogens causing ventilator-associated pneumonia (VAP) has resulted in higher hospital costs, longer hospital stays, and increased hospital mortality. Biofilms in the endotracheal tube of ventilated patients act as protective shield from host immunity. They induce chronic and recurrent infections that defy common antibiotics. This study intended to determine the biofilm produced by pathogens causing VAP and their relation with drug resistance. Methods. Bronchoalveolar lavage and deep tracheal aspirates (n =70) were obtained from the patients mechanically ventilated for more than 48 hours in the intensive care units of Tribhuvan University Teaching Hospital, Kathmandu, and processed according to the protocol of the American Society for Microbiology (ASM). -
Helicobacter Pylori: Comparative Genomics and Structure-Function Analysis of the Flagellum Biogenesis Protein HP0958
UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958 Author(s) de Lacy Clancy, Ceara A. Publication date 2014 Original citation de Lacy Clancy, C. A. 2014. Helicobacter pylori: comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2014, Ceara A. De Lacy Clancy. http://creativecommons.org/licenses/by-nc-nd/3.0/ Item downloaded http://hdl.handle.net/10468/1684 from Downloaded on 2021-10-10T14:33:51Z Helicobacter pylori: Comparative genomics and structure-function analysis of the flagellum biogenesis protein HP0958 A Thesis Presented in Partial Fulfilment of the Requirements for the Degree of Doctor of Philosophy by Ceara de Lacy Clancy, B.Sc. School of Microbiology National University of Ireland, Cork Supervisor: Prof. Paul W. O’Toole Head of School of Microbiology: Prof. Gerald Fitzgerald February 2014 Table of Contents Table of Contents Abstract ........................................................................................................................ i Chapter 1 Literature Review....................................................................................................... 1 1 Helicobacter pylori .................................................................................................. 2 1.1 Discovery -
Campylobacter (C
GI Panel Limitations: Copied from the BioFire GI Panel Package Insert. RFIT-PRT-0143-04 June 2017 Include in all sections: This test is a qualitative test and does not provide a quantitative value for the organism(s) in the sample. The performance of this test has not been established for patients without signs and symptoms of gastrointestinal illness. Virus, bacteria, and parasite nucleic acid may persist in vivo independently of organism viability. Additionally, some organisms may be carried asymptomatically. Detection of organism targets does not imply that the corresponding organisms are infectious or are the causative agents for clinical symptoms. Virus, bacteria, and parasite nucleic acid may persist in vivo independently of organism viability. Additionally, some organisms may be carried asymptomatically. Detection of organism targets does not imply that the corresponding organisms are infectious or are the causative agents for clinical symptoms. A negative FilmArray GI Panel result does not exclude the possibility of gastrointestinal infection. Negative test results may occur from sequence variants in the region targeted by the assay, the presence of inhibitors, technical error, sample mix-up, or an infection caused by an organism not detected by the panel. Test results may also be affected by concurrent antimicrobial therapy or levels of organism in the sample that are below the limit of detection for the test. Negative results should not be used as the sole basis for diagnosis, treatment, or other management decisions. The performance of this test has not been evaluated for immunocompromised individuals. Campylobacter (C. jejuni/C. coli/C. upsaliensis) The FilmArray GI Panel contains two assays (Campy 1 and Campy 2) designed to together detect, but not differentiate, the most common Campylobacter species associated with human gastrointestinal illness: C. -
Analysis of Sequence Variation at Two Helicobacter Pylori Genetic Loci Potentially Involved in Virulence
W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2008 Analysis of Sequence Variation at Two Helicobacter pylori Genetic Loci Potentially involved in Virulence George Warren Liechti College of William & Mary - Arts & Sciences Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Microbiology Commons, and the Molecular Biology Commons Recommended Citation Liechti, George Warren, "Analysis of Sequence Variation at Two Helicobacter pylori Genetic Loci Potentially involved in Virulence" (2008). Dissertations, Theses, and Masters Projects. Paper 1539626867. https://dx.doi.org/doi:10.21220/s2-zrbg-b193 This Thesis is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Analysis of sequence variation atHelicobacter two pylori genetic loci potentially involved in virulence. George Warren Liechti Springfield, Virginia Bachelors of Science, College of William and Mary, 2003 A Thesis presented to the Graduate Faculty of the College of William and Mary in Candidacy for the Degree of Master of Science Department of Biology The College of William and Mary May, 2008 APPROVAL PAGE This Thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science George Warren Liechti Approved by^the Cq , April, 2008 Committee Chair Associate Professor Mark Forsyth, Biology, The College of William and Mary r Professor Margaret Saha, Biology, The College of William and Mary Associate Professor George Gilchrist, Biology, The College of William and Mary / J / ABSTRACT PAGE Helicobacter pylori colonizes the gastric mucosa of nearly half the world’s population and is a well documented etiologic agent of peptic ulcer disease (PUD) and a significant risk factor for the development of gastric cancer. -
Antimicrobial Resistance in Wound Infections, Ghana, 2014
Article DOI: https://doi.org/10.3201/eid2405.171506 Antimicrobial Resistance in Wound Infections, Ghana, 2014 Technical Appendix Technical Appendix Table 1. Site and mode of acquisition of wound infection in 67 patients, rural Ghana Localization No. of patients Acquisition upper extremity abscess over shoulder 1 community-acquired abscess of finger 1 community-acquired infection of palm injury 1 community-acquired infection of lower arm injury 1 community-acquired trunk/head abscess of cheek 2 community-acquired abscess of back 2 community-acquired abscess of abdominal wall 2 community-acquired ulcerated mastitis 2 community-acquired ulcerated tumor over scapula 1 community-acquired infected herniotomy wound epigastric 2 hospital-acquired infected herniotomy wound inguinal 1 hospital-acquired syringe abscess of buttocks 2 hospital-acquired ulcerated scrotum tumor 1 community-acquired lower extremity cellulitis 6 community-acquired infected skin graft 4 hospital-acquired infected entry wound of Steinmann-pin 2 hospital-acquired infected entry wound of external fixator 1 hospital-acquired infected injury of toe 2 community-acquired infected injury of foot 3 community-acquired infected injury of lower leg 7 community-acquired infected injury of upper leg 4 community-acquired abscess of upper leg 1 community-acquired infected ulcer of foot 8 community-acquired abscess of foot 1 community-acquired laparotomy wound laparotomy wound 9 hospital-acquired Technical Appendix Table 2. Detected bacterial species in monomicrobial and polymicrobial -
Comparative Analyses of Whole-Genome Protein Sequences
www.nature.com/scientificreports OPEN Comparative analyses of whole- genome protein sequences from multiple organisms Received: 7 June 2017 Makio Yokono 1,2, Soichirou Satoh3 & Ayumi Tanaka1 Accepted: 16 April 2018 Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several Published: xx xx xxxx methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are diferent than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufcient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms. Te reconstruction of phylogenetic trees is a powerful tool for understanding organismal evolutionary processes. Molecular phylogenetic analysis using ribosomal RNA (rRNA) clarifed the phylogenetic relationship of the three domains, bacterial, archaeal, and eukaryotic1.