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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. -
Kongre Kitabı
Book of Abstracts International VETistanbul Group Congress 2014 28-30 April, 2014 Istanbul, Turkey Book of Abstracts www.vetistanbul2014.org International VETistanbul Group Congress 2014 28-30 April 2014 International VETistanbul Group Congress 2014 28-30 April, 2014 Istanbul, Turkey Organizing Committee Prof. Dr. Halil GÜNEŞ, Chair Prof. Dr. Bülent EKİZ Prof. Dr. Ali AYDIN Assoc. Prof. Dr. Serkan İKİZ Assoc. Prof. Dr. Hasret DEMİRCAN YARDİBİ Assoc. Prof. Dr. Gülsün PAZVANT Scientific Committee* Prof. Dr. Kemal AK, Turkey Prof. Dr. Anatoliy ALEXANDROVICH STEKOLNIKOV, Russia Prof. Dr. Bogdan AMINKOV, Bulgaria Prof. Dr. Geno ATASANOV ANGELOV, Bulgaria Prof. Dr. Hajrudin BESIROVIC, Bosnia and Herzegovina Prof. Dr. Nihad FEJZIC, Bosnia and Herzegovina Assoc. Prof. Dr. Plamen GEORGIEV, Bulgaria Prof. Dr. Zehra HAJRULAI MUSLIU, Macedonia Assoc. Prof. Dr. Afrim HAMIDI, Kosovo Prof. Dr. Telman ISKENDEROV, Azerbaijan Prof. Dr. Larisa KARPENKO, Russia Prof. Dr. Ismail KIRSAN, Turkey Prof. Dr. Mihni LYUTSKANOV, Bulgaria Assoc. Prof. Dr. Avni ROBAJ, Kosovo Prof. Dr. Velimir STOJKOVSKI, Macedonia Prof. Dr. Semsir VELIYEV, Azerbaijan *Alphabetically listed by the according to the family name Scientific Secreteria Prof. Dr. Bülent EKİZ, Turkey Dr. Karlo MURATOĞLU, Turkey International VETistanbul Group Congress 2014, 28-30 April, Istanbul, Turkey IV International VETistanbul Group Congress 2014 28-30 April 2014 Dear Respectable Colleagues and Guests, First of all, I greet you all with my heart. Also, I would like to thank you for taking place on our side due to the contribution given to the establishment of VETistanbul Group. Known as, VETistanbul Group was established, under the coordination of Istanbul University, with joint decision of Veterinary Faculty of the University of Sarajevo, Saint Petersburg State Academy of Veterinary Medicine, Stara Zagora Trakia University, Ss. -
Review: Other Helicobacter Species
DOI: 10.1111/hel.12645 SUPPLEMENT ARTICLE Review: Other Helicobacter species Armelle Ménard1 | Annemieke Smet2 1INSERM, UMR1053, Bordeaux Research in Translational Oncology, BaRITOn, Université Abstract de Bordeaux, Bordeaux, France This article is a review of the most important, accessible, and relevant literature pub‐ 2 Laboratorium of Experimental lished between April 2018 and April 2019 in the field of Helicobacter species other than Medicine and Pediatrics, Department of Translational Research in Immunology and Helicobacter pylori. The initial part of the review covers new insights regarding the pres‐ Inflammation, Faculty of Medicine and ence of gastric and enterohepatic non‐H. pylori Helicobacter species (NHPH) in humans Health Sciences, University of Antwerp, Wilrijk (Antwerp), Belgium and animals, while the subsequent section focuses on the progress in our understand‐ ing of the pathogenicity and evolution of these species. Over the last year, relatively Correspondence Armelle Ménard, Laboratoire de few cases of gastric NHPH infections in humans were published, with most NHPH in‐ Bactériologie, INSERM U1053, Campus de fections being attributed to enterohepatic Helicobacters. A novel species, designated Carreire, Université de Bordeaux, Bâtiment 2B RDC ‐ Case 76, 146 rue Léo Saignat, “Helicobacter caesarodunensis,” was isolated from the blood of a febrile patient and F33076 Bordeaux, France. numerous cases of human Helicobacter cinaedi infections underlined this species as a Email: Armelle.Menard@u‐bordeaux.fr true emerging pathogen. With regard to NHPH in animals, canine/feline gastric NHPH cause little or no harm in their natural host; however they can become opportunistic when translocated to the hepatobiliary tract. The role of enterohepatic Helicobacter species in colorectal tumors in pets has also been highlighted. -
Studies on the Detection Methods of Campylobacter and Faecal Indicator Bacteria in Drinking Water
Tarja Pitkänen Tarja Pitkänen Tarja Studies on the Detection Tarja Pitkänen Methods of Campylobacter RESEARCH Studies on the Detection Methods of RESEARCH Campylobacter and Faecal Indicator Bacteria and Faecal Indicator in Drinking Water Bacteria in Drinking Water Indicator Bacteria in Drinking Water Drinking in Bacteria Indicator Methods Detection the on Studies Faecal contamination of drinking water and subsequent waterborne gastrointestinal infection outbreaks are a major public health concern. In this study, faecal indicator bacteria were detected in 10% of the groundwater samples analysed. The main on-site hazards to water safety at small community water supplies included inadequate well construction and maintenance, an insufficient depth of the protective soil layer and bank filtration. As a preventive measure, the upgrading of the water treatment processes and utilization of disinfection at small Finnish groundwater supplies are recommended. More efficient and specific and less time-consuming methods for enumeration and typing of E. coli and coliform bacteria from non-disinfected water as well as for cultivation and molecular detection and typing of Campylobacter were found in the study. These improvements in methodology for the analysis of the faecal bacteria from water might promote public health protection as they Campylobacter could be anticipated to result in very important time savings and improve the tracking of faecal contamination source in waterborne outbreak investigations. and Faecal Faecal and .!7BC5<2"HIGEML! National Institute for Health and Welfare P.O. Box 30 (Mannerheimintie 166) FI-00271 Helsinki, Finland Telephone: +358 20 610 6000 39 ISBN 978-952-245-319-8 39 2010 39 www.thl.fi Tarja Pitkänen Studies on the Detection Methods of Campylobacter and Faecal Indicator Bacteria in Drinking Water ACADEMIC DISSERTATION To be presented with the permission of the Faculty of Science and Forestry of the University of Eastern Finland for public examination in auditorium, MediTeknia Building, on October 1st, 2010 at 12 o’clock noon. -
C O N F E R E N C E 22 27 April 2016
Joint Pathology Center Veterinary Pathology Services WEDNESDAY SLIDE CONFERENCE 2015-2016 C o n f e r e n c e 22 27 April 2016 Cory Brayton, DVM, Ph.D., DACVP Associate Professor, Molecular & Comparative Pathobiology Johns Hopkins University School of Medicine Broadway Research Building, Suite 851 733 North Broadway Baltimore, MD 21205 CASE I: NIEHS-087 (JPC 4017222). Signalment: 11-month-old B6.129S- Cybbtm1Din/J mouse (Mus musculus) History: A breeding colony of B6.129S- Cybbtm1Din/J mice were housed in an AAALAC International accredited facility. The mice were housed in static micro isolator cases with ad libitum autoclaved food (NIH-31) and beta chip bedding. Mice were provided acidified water due to imm- unocompromised state. The mice were Body as a while, mouse. The liver was slightly enlarged, housed in the same room as B6 imm- and there are multiple tan foci in the liver and lung. (Photo courtesy of: National Institute of Environmental unocompetent mice. Sudden deaths were Health Sciences, Cellular and Molecular Pathology noted in the colony over a weekend. A total Branch and Comparative Medicine Branch, P.O. Box of 87 mice, aged from one to eleven months 12233, Research Triangle Park, NC 27709, http://www.niehs.nih.gov/research/atniehs/labs/lep/index. were affected. Of these, 45 mice were found cfm) dead and 19 sick mice were euthanized and were multifocal tan foci in the liver, spleen necropsied. Twenty males and 38 females and lung. were affected. Laboratory Results: From multiple tissues, Gross Pathology: The livers were pale and a pure culture of Burkholderia spp. -
A Focus on Protein Glycosylation in Lactobacillus
International Journal of Molecular Sciences Review How Sweet Are Our Gut Beneficial Bacteria? A Focus on Protein Glycosylation in Lactobacillus Dimitrios Latousakis and Nathalie Juge * Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK; [email protected] * Correspondence: [email protected]; Tel.: +44-(0)-160-325-5068; Fax: +44-(0)-160-350-7723 Received: 22 November 2017; Accepted: 27 December 2017; Published: 3 January 2018 Abstract: Protein glycosylation is emerging as an important feature in bacteria. Protein glycosylation systems have been reported and studied in many pathogenic bacteria, revealing an important diversity of glycan structures and pathways within and between bacterial species. These systems play key roles in virulence and pathogenicity. More recently, a large number of bacterial proteins have been found to be glycosylated in gut commensal bacteria. We present an overview of bacterial protein glycosylation systems (O- and N-glycosylation) in bacteria, with a focus on glycoproteins from gut commensal bacteria, particularly Lactobacilli. These emerging studies underscore the importance of bacterial protein glycosylation in the interaction of the gut microbiota with the host. Keywords: protein glycosylation; gut commensal bacteria; Lactobacillus; glycoproteins; adhesins; lectins; O-glycosylation; N-glycosylation; probiotics 1. Introduction Protein glycosylation, i.e., the covalent attachment of a carbohydrate moiety onto a protein, is a highly ubiquitous protein modification in nature, and considered to be one of the post-translational modifications (PTM) targeting the most diverse group of proteins [1]. Although it was originally believed to be restricted to eukaryotic systems and later to archaea, it has become apparent nowadays that protein glycosylation is a common feature in all three domains of life. -
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. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
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. -
Supplemental Material S1.Pdf
Phylogeny of Selenophosphate synthetases (SPS) Supplementary Material S1 ! SelD in prokaryotes! ! ! SelD gene finding in sequenced prokaryotes! We downloaded a total of 8263 prokaryotic genomes from NCBI (see Supplementary Material S7). We scanned them with the program selenoprofiles (Mariotti 2010, http:// big.crg.cat/services/selenoprofiles) using two SPS-family profiles, one prokaryotic (seld) and one mixed eukaryotic-prokaryotic (SPS). Selenoprofiles removes overlapping predictions from different profiles, keeping only the prediction from the profile that seems closer to the candidate sequence. As expected, the great majority of output predictions in prokaryotic genomes were from the seld profile. We will refer to the prokaryotic SPS/SelD !genes as SelD, following the most common nomenclature in literature.! To be able to inspect results by hand, and also to focus on good-quality genomes, we considered a reduced set of species. We took the prok_reference_genomes.txt list from ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/, which NCBI claims to be a "small curated subset of really good and scientifically important prokaryotic genomes". We named this the prokaryotic reference set (223 species - see Supplementary Material S8). We manually curated most of the analysis in this set, while we kept automatized the !analysis on the full set.! We detected SelD proteins in 58 genomes (26.0%) in the prokaryotic reference set (figure 1 in main paper), which become 2805 (33.9%) when considering the prokaryotic full set (figure SM1.1). The difference in proportion between the two sets is due largely to the presence of genomes of very close strains in the full set, which we consider redundant. -
Co-Infection Associated with Diarrhea in a Colony of <I>Scid
Laboratory Animal Science Vol 48, No 5 Copyright 1998 October 1998 by the American Association for Laboratory Animal Science Helicobacter bilis/Helicobacter rodentium Co-Infection Associated with Diarrhea in a Colony of scid Mice Nirah H. Shomer,* Charles A. Dangler, Robert P. Marini, and James G. Fox† Abstract _ An outbreak of diarrhea spanning 3 months occurred in a breeding colony of scid/Trp53 knockout mice. Approximately a third of the 150 mice were clinically affected, with signs ranging from mucoid or watery diarrhea to severe hemorrhagic diarrhea with mortality. Helicobacter bilis and the newly recognized urease-negative organ- ism H. rodentium were isolated from microaerobic culture of feces or cecal specimens from affected mice. Dual infection with H. bilis and H. rodentium were confirmed by culture and polymerase chain reaction (PCR) in several animals. Both Helicobacter species rapidly colonized immunocompetent sentinel mice exposed to bedding from cages containing affected mice, but the sentinel remained asymptomatic. Mice with diarrhea had multifocal to segmental proliferative typhlitis, colitis, and proctitis. Several affected mice had multifocal mucosal necrosis with a few focal ulcers in the cecum, colon, and rectum. Mice with diarrhea were treated with antibiotic food wafers (1.5 mg of amoxicillin, 0.69 mg of metronidazole, and 0.185 mg of bismuth/mouse per day) previously shown to eradi- cate H. hepaticus in immunocompetent mice. Antibiotic treatment resulted in resolution of diarrhea, but not eradication of H. bilis and H. rodentium; mice continued to have positive PCR results after a 2-week treatment regimen, and clinical signs of diarrhea returned in some mice when treatment was suspended.