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Liu C, Mesman R, Pol A, Angius F, Op den Camp HJM. Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV. Antonie Van Leeuwenhoek 2023; 116:1227-1245. [PMID: 37737555 PMCID: PMC10542722 DOI: 10.1007/s10482-023-01879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria against a hostile environment. The proteins embedded in the OM fulfil a number of tasks that are crucial to the bacterial cell. In this study, we identified and characterised a major outer membrane protein (WP_009059494) from Methylacidiphilum fumariolicum SolV. PRED-TMBB and AlphaFold2 predicted this protein to form a porin with a β-barrel structure consisting of ten antiparallel β-sheets and with a small amphipathic N-terminal α-helix in the periplasm. We purified soluble recombinant protein WP_009059494 from E. coli using Tris-HCl buffer with SDS. Antibodies were raised against two peptides in the two large extracellular loops of protein WP_009059494 and immunogold localisation showed this protein to be mainly present in the OM of strain SolV. In addition, this protein is tightly associated with the OM, and is resistant to extraction. Only a small amount can be isolated from the cell envelope using harsh conditions (SDS and boiling). Despite this resistance to extraction, WP_009059494 most likely is an outer membrane protein. A regular lattice could not be detected by negative staining TEM of strain SolV and isolated protein WP_009059494. Considering the specific ecological niche of strain SolV living in a geothermal environment with low pH and high temperatures, this major protein WP_009059494 may act as barrier to resist the extreme conditions found in its natural environment. In addition, we found an absence of the BamB, BamC and BamE proteins of the canonical BAM complex, in Methylacidiphilum and Methylacidimicrobium species. This suggests that these bacteria use a simple BAM complex for folding and transport of OM proteins.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Rob Mesman
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands.
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Bladder epithelial cell phosphate transporter inhibition protects mice against uropathogenic Escherichia coli infection. Cell Rep 2022; 39:110698. [PMID: 35443182 DOI: 10.1016/j.celrep.2022.110698] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/12/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
Urinary tract infections are predominantly caused by uropathogenic Escherichia coli (UPEC). UPEC infects bladder epithelial cells (BECs) via fusiform vesicles, escapes into the cytosol to evade exocytosis, and establishes intracellular bacterial communities (IBCs) for the next round of infection. The UPEC vesicle escape mechanism remains unclear. Here we show that UPEC senses host immune responses and initiates escape by upregulating a key phospholipase. The UPEC phospholipase PldA disrupts the vesicle membrane, and pldA expression is activated by phosphate reduction in vesicles. The host phosphate transporter PIT1 is located on the fusiform vesicle membrane, transporting phosphate into the cytosol. UPEC infection upregulates PIT1 via nuclear factor κB (NF-κB), resulting in phosphate reduction. Silencing PIT1 blocks UPEC vesicle escape in BECs, inhibits IBC formation in mouse bladders, and protects mice from UPEC infection. Our results shed light on pathogenic bacteria responding to intracellular phosphate shortage and tackling host defense and provide insights for development of new therapeutic agents to treat UPEC infection.
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Shigella Outer Membrane Vesicles as Promising Targets for Vaccination. Int J Mol Sci 2022; 23:ijms23020994. [PMID: 35055181 PMCID: PMC8781765 DOI: 10.3390/ijms23020994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
The clinical symptoms of shigellosis, a gastrointestinal infection caused by Shigella spp. range from watery diarrhea to fulminant dysentery. Endemic infections, particularly among children in developing countries, represent the majority of clinical cases. The situation is aggravated due to the high mortality rate of shigellosis, the rapid dissemination of multi-resistant Shigella strains and the induction of only serotype-specific immunity. Thus, infection prevention due to vaccination, encompassing as many of the circulating serotypes as possible, has become a topic of interest. However, vaccines have turned out to be ineffective so far. Outer membrane vesicles (OMVs) are promising novel targets for vaccination. OMVs are constitutively secreted by Gram-negative bacteria including Shigella during growth. They are composed of soluble luminal portions and an insoluble membrane and can contain toxins, bioactive periplasmic and cytoplasmic (lipo-) proteins, (phospho-) lipids, nucleic acids and/or lipopolysaccharides. Thus, OMVs play an important role in bacterial cell–cell communication, growth, survival and pathogenesis. Furthermore, they modulate the secretion and transport of biomolecules, the stress response, antibiotic resistance and immune responses of the host. Thus, OMVs serve as novel secretion machinery. Here, we discuss the current literature and highlight the properties of OMVs as potent vaccine candidates because of their immunomodulatory, antigenic and adjuvant properties.
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Dell’Annunziata F, Folliero V, Giugliano R, De Filippis A, Santarcangelo C, Izzo V, Daglia M, Galdiero M, Arciola CR, Franci G. Gene Transfer Potential of Outer Membrane Vesicles of Gram-Negative Bacteria. Int J Mol Sci 2021; 22:ijms22115985. [PMID: 34205995 PMCID: PMC8198371 DOI: 10.3390/ijms22115985] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The increasing spread of multidrug-resistant pathogenic bacteria is one of the major threats to public health worldwide. Bacteria can acquire antibiotic resistance and virulence genes through horizontal gene transfer (HGT). A novel horizontal gene transfer mechanism mediated by outer membrane vesicles (OMVs) has been recently identified. OMVs are rounded nanostructures released during their growth by Gram-negative bacteria. Biologically active toxins and virulence factors are often entrapped within these vesicles that behave as molecular carriers. Recently, OMVs have been reported to contain DNA molecules, but little is known about the vesicle packaging, release, and transfer mechanisms. The present review highlights the role of OMVs in HGT processes in Gram-negative bacteria.
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Affiliation(s)
- Federica Dell’Annunziata
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Veronica Folliero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Rosa Giugliano
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Cristina Santarcangelo
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy; (C.S.); (M.D.)
| | - Viviana Izzo
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, 84081 Salerno, Italy;
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131 Naples, Italy; (C.S.); (M.D.)
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania Luigi Vanvitelli, 80138 Naples, Italy; (F.D.); (V.F.); (R.G.); (A.D.F.); (M.G.)
| | - Carla Renata Arciola
- Research Unit on Implant Infections, Laboratorio di Patologia delle Infezioni Associate all’Impianto, IRCCS Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Correspondence: (C.R.A.); (G.F.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, 84081 Salerno, Italy;
- Correspondence: (C.R.A.); (G.F.)
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Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application. CRYSTALS 2019. [DOI: 10.3390/cryst9110597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
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Baarda BI, Martinez FG, Sikora AE. Proteomics, Bioinformatics and Structure-Function Antigen Mining For Gonorrhea Vaccines. Front Immunol 2018; 9:2793. [PMID: 30564232 PMCID: PMC6288298 DOI: 10.3389/fimmu.2018.02793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the serious health consequences combined with the prevalence and the dire possibility of untreatable gonorrhea. Reverse vaccinology, which includes genome and proteome mining, has proven successful in the discovery of vaccine candidates against many pathogenic bacteria. Here, we describe proteomic applications including comprehensive, quantitative proteomic platforms and immunoproteomics coupled with broad-ranging bioinformatics that have been applied for antigen mining to develop gonorrhea vaccine(s). We further focus on outlining the vaccine candidate decision tree, describe the structure-function of novel proteome-derived antigens as well as ways to gain insights into their roles in the cell envelope, and underscore new lessons learned about the fascinating biology of Neisseria gonorrhoeae.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Fabian G. Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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Stead CM, Cockrell DC, Beare PA, Miller HE, Heinzen RA. A Coxiella burnetii phospholipase A homolog pldA is required for optimal growth in macrophages and developmental form lipid remodeling. BMC Microbiol 2018; 18:33. [PMID: 29661138 PMCID: PMC5902883 DOI: 10.1186/s12866-018-1181-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/09/2018] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Many gram-negative bacteria produce an outer membrane phospholipase A (PldA) that plays an important role in outer membrane function and is associated with virulence. RESULTS In the current study, we characterized a pldA mutant of Coxiella burnetii, an intracellular gram-negative pathogen and the agent of human Q fever. The C. burnetti pldA open reading frame directs synthesis of a protein with conserved PldA active site residues. A C. burnetii ΔpldA deletion mutant had a significant growth defect in THP-1 macrophages, but not axenic medium, that was rescued by complementation. Thin layer chromatography was employed to assess whether pldA plays a role in remodeling membrane lipids during C. burnetii morphological differentiation. Extracted lipids were analyzed from replicating, logarithmic phase large cell variants (LCVs), non-replicating, stationary phase small cell variants (SCVs), and a mixture of LCVs and SCVs. Similar to Escherichia coli, all three forms contained cardiolipin (CL), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). However, PE and PG were present in lower quantities in the SCV while three additional lipid species were present in higher quantities. Co-migration with standards tentatively identified two of the three SCV-enriched lipids as lyso-phosphatidylethanolamine, a breakdown product of PE, and free fatty acids, which are generally toxic to bacteria. Developmental form lipid modifications required the activity of PldA. CONCLUSIONS Collectively, these results indicate developmentally-regulated lipid synthesis by C. burnetii contributes to colonization of macrophages and may contribute to the environmental stability and the distinct biological properties of the SCV.
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Affiliation(s)
- Christopher M. Stead
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
- Department of Chemistry, New Mexico Highlands University, Las Vegas, New Mexico USA
| | - Diane C. Cockrell
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Paul A. Beare
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Heather E. Miller
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
| | - Robert A. Heinzen
- Coxiella Pathogenesis Section, Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana USA
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Pastor Y, Camacho A, Gil AG, Ramos R, Ceráin ALD, Peñuelas I, Irache JM, Gamazo C. Effective protection of mice against Shigella flexneri with a new self-adjuvant multicomponent vaccine. J Med Microbiol 2017; 66:946-958. [PMID: 28721849 DOI: 10.1099/jmm.0.000527] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
PURPOSE The aim of this study was to develop an immunogenic protective product against Shigella flexneri by employing a simple and safe heat treatment-based strategy. METHODOLOGY The physicochemical characteristics of naturally produced (OMV) and heat-induced (HT) outer-membrane vesicles from S. flexneri were examined, including a comparison of the protein content of the products. Toxicological and biodistribution studies, and a preliminary experiment to examine the protective effectiveness of HT in a murine model of S. flexneri infection, were also included. RESULTS This method simultaneously achieves complete bacterial inactivation and the production of the HT vaccine product, leading to a safe working process. The obtained HT complex presented a similar morphology (electron microscopy) and chemical composition to the classical OMV, although it was enriched in some immunogens, such as lipoproteins, OmpA or OmpC, among others. The HT formulation was not toxic and biodistribution studies performed in mice demonstrated that the vaccine product remained in the small intestine after nasal administration. Finally, a single dose of HT administered nasally was able to protect mice against S. flexneri 2a. CONCLUSION The convenient and safe manufacturing process, and the preliminary biological evaluation, support the use of the self-adjuvanted HT complex as a new vaccine candidate to face shigellosis. Further development is required, such as additional immune analyses, to evaluate whether this new subunit vaccine can be useful in achieving full protection against Shigella.
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Affiliation(s)
- Yadira Pastor
- Department of Microbiology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
| | - Ana Camacho
- Department of Microbiology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
| | - Ana Gloria Gil
- Department of Toxicology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
| | - Rocío Ramos
- Department of Nuclear Medicine, Clínica Universidad de Navarra, Institute of Tropical Health, University of Navarra 31008, Pamplona, Spain
| | - Adela López de Ceráin
- Department of Toxicology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
| | - Iván Peñuelas
- Department of Nuclear Medicine, Clínica Universidad de Navarra, Institute of Tropical Health, University of Navarra 31008, Pamplona, Spain
| | - Juan M Irache
- Department of Pharmaceutical Technology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
| | - Carlos Gamazo
- Department of Microbiology, Institute of Tropical Health, University of Navarra, 31008 Pamplona, Spain
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Vollan HS, Tannæs T, Caugant DA, Vriend G, Bukholm G. Outer membrane phospholipase A's roles in Helicobacter pylori acid adaptation. Gut Pathog 2017; 9:36. [PMID: 28616083 PMCID: PMC5469174 DOI: 10.1186/s13099-017-0184-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/08/2017] [Indexed: 02/08/2023] Open
Abstract
Background The pH of the human gastric mucosa varies around 2.5 so that only bacteria with strong acidic stress tolerance can colonize it. The ulcer causing Helicobacter pylori thrives in the gastric mucosa. We analyse the roles of the key outer membrane protein OMPLA in its roles in acid tolerance. Results The homology model of Helicobacter pylori outer membrane phospholipase A (OMPLA) reveals a twelve stranded β-barrel with a pore that allows molecules to pass with a diameter up to 4 Å. Structure based multiple sequence alignments revealed the functional roles of many amino acids, and led to the suggestion that OMPLA has multiple functions. Besides its role as phospholipase it lets urea enter and ammonium exit the periplasm. Combined with an extensive literature study, our work leads to a comprehensive model for H. pylori’s acid tolerance. This model is based on the conversion of urea into ammonium, and it includes multiple roles for OMPLA and involves two hitherto little studied membrane channels in the OMPLA operon. Conclusion The three-dimensional model of OMPLA predicts a transmembrane pore that can aid H. pylori’s acid tolerance through urea influx and ammonium efflux. After urea passes through OMPLA into the periplasm, it passes through the pH-gated inner membrane channel UreI into the cytoplasm where urease hydrolyses it into NH3 and CO2. Most of the NH3 becomes NH4+ that is likely to need an inner membrane channel to reach the periplasm. Two genes that are co-regulated with OMPLA in gastric Helicobacter operons could aid this transport. The NH4+ that might leave the cell through the OMPLA pore has been implicated in H. pylor’s pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0184-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hilde S Vollan
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, 1478 Lørenskog, Norway.,Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway
| | - Tone Tannæs
- Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, PO box 28, 1478 Lørenskog, Norway
| | - Dominique A Caugant
- Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway.,Department of Community Medicine and Global Health, Faculty of Medicine, University of Oslo, P.O. Box 1130, Blindern, 0318 Oslo, Norway
| | - Gert Vriend
- CMBI, Radboudumc, 6525 GA Nijmegen, The Netherlands
| | - Geir Bukholm
- Norwegian Institute of Public Health, Box 4404, Nydalen, 0403 Oslo, Norway.,Norwegian University of Life Sciences, PO Box 5003, 1430 Ås, Norway
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