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Article ; Online: Comparative study of embedded functionalised MWCNTs and GO in Ultrafiltration (UF) PVC membrane: interaction mechanisms and performance

Sadiq, Amna J. / Awad, Eman S. / Shabeeb, Kadhum M. / Khalil, Bassam I. / Al-Jubouri, Sama M. / Sabirova, T. M. / Tretyakova, N. A. / Majdi, Hasan Shaker / Alsalhy, Qusay F. / Braihi, Auda J.

International Journal of Environmental Analytical Chemistry. 2023 Jan. 26, v. 103, no. 2 p.415-436

2023

Abstract: This work presents the development of polyvinyl chloride/functionalised multi-carbon nanotube (PVC/F-MWCNT) membranes and PVC/graphene oxide (PVC/GO) membranes for the improved removal of chemical oxygen demand (COD) from actual petroleum wastewater. ... ...

Abstract	This work presents the development of polyvinyl chloride/functionalised multi-carbon nanotube (PVC/F-MWCNT) membranes and PVC/graphene oxide (PVC/GO) membranes for the improved removal of chemical oxygen demand (COD) from actual petroleum wastewater. Also, this work for the first time presents the proposed interaction mechanism between the contents of PVC/GO and PVC/F-MWCNT membranes as well as the interaction mechanism of each composite membrane with water molecules. The effect of both F-MWCNT and GO content on the characteristics and performance of the PVC/F-MWCNT membrane and PVC/GO membrane were studied. Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM), atomic force microscopy (AFM), contact angle (CA), differential scanning calorimetry (DSC), porosity and tensile strength were used to examine the properties of F-MWCNT, GO, PVC/F-MWCNT and PVC/GO membranes. The composite membranes’ performance was studied by measuring the rejection of chemical oxygen demand (COD) and mass flux. It was found that F-MWCNTs and GO played significant roles in the membranes’ structural morphology. A significant improvement was obtained in the CA, porosity and tensile strength of the membranes by embedding the PVC casting solution with 0.12 wt% of each F-MWCNTand GO. The PVC/F-MWCNTs membrane showed higher performance in term of mass flux and COD rejection that reached 88.9%, which makes using a PVC/F-MWCNTs membrane preferable to remove COD from petroleum wastewater.
Keywords	Fourier transform infrared spectroscopy ; X-ray diffraction ; analytical chemistry ; asymmetric membranes ; atomic force microscopy ; calorimetry ; chemical oxygen demand ; comparative study ; contact angle ; graphene oxide ; mass transfer ; nanotubes ; petroleum ; poly(vinyl chloride) ; porosity ; tensile strength ; ultrafiltration ; wastewater ; Interaction mechanism ; MWCNTs ; modified membrane ; flat-sheet membrane ; COD removal
Language	English
Dates of publication	2023-0126
Size	p. 415-436.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	120480-4
ISSN	1029-0397 ; 0306-7319 ; 0092-9085
ISSN (online)	1029-0397
ISSN	0306-7319 ; 0092-9085
DOI	10.1080/03067319.2020.1858073
Database	NAL-Catalogue (AGRICOLA)

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Article: Enzymes Catalyzing the TCA- and Urea Cycle Influence the Matrix Composition of Biofilms Formed by Methicillin-Resistant

De Backer, Sarah / Sabirova, Julia / De Pauw, Ines / De Greve, Henri / Hernalsteens, Jean-Pierre / Goossens, Herman / Malhotra-Kumar, Surbhi

Microorganisms

2018 Volume 6, Issue 4

Abstract: In methicillin- ... ...

Abstract	In methicillin-sensitive
Language	English
Publishing date	2018-10-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms6040113
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Exosomal Release of L-Plastin by Breast Cancer Cells Facilitates Metastatic Bone Osteolysis.

Tiedemann, Kerstin / Sadvakassova, Gulzhakhan / Mikolajewicz, Nicholas / Juhas, Michal / Sabirova, Zarina / Tabariès, Sébastien / Gettemans, Jan / Siegel, Peter M / Komarova, Svetlana V

Translational oncology

2018 Volume 12, Issue 3, Page(s) 462–474

Abstract: Bone metastasis from breast and prostate carcinomas is facilitated by activation of bone-resorbing osteoclasts. Using proteomics approaches, we have identified peroxiredoxin-4 (PRDX4) as a cancer-secreted mediator of osteoclastogenesis. We now report ... ...

Abstract	Bone metastasis from breast and prostate carcinomas is facilitated by activation of bone-resorbing osteoclasts. Using proteomics approaches, we have identified peroxiredoxin-4 (PRDX4) as a cancer-secreted mediator of osteoclastogenesis. We now report characterization of L-plastin in the conditioned media (CM) of MDA-MB-231 human breast cancer cells using immunoblotting and mass spectrometry. The osteoclastogenic potential of MDA-MB-231 CM with siRNA-silenced L-plastin was significantly reduced. L-plastin was detected in cancer-derived exosomes, and inhibition of exosomal release significantly decreased the osteoclastogenic capacity of MDA-MB-231 CM. When added to osteoclast precursors primed with RANKL for 2 days, recombinant L-plastin induced calcium/NFATc1-mediated osteoclastogenesis to the levels similar to continuous treatment with RANKL. Using shRNA, we generated MDA-MB-231 cells lacking L-plastin, PRDX4, or both and injected these cell populations intratibially in CD-1 immunodeficient mice. Micro-CT and histomorphometric analysis demonstrated a complete loss of osteolysis when MDA-MB-231 cells lacking both L-plastin and PRDX4 were injected. A meta-analysis established an increase in L-plastin and PRDX4 mRNA expression in numerous human cancers, including breast and prostate carcinomas. This study demonstrates that secreted L-plastin and PRDX4 mediate osteoclast activation by human breast cancer cells.
Language	English
Publishing date	2018-12-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2443840-6
ISSN	1936-5233 ; 1936-5233 ; 1944-7124
ISSN (online)	1936-5233
ISSN	1936-5233 ; 1944-7124
DOI	10.1016/j.tranon.2018.11.014
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Article: Complete Genome Sequences of Two Prolific Biofilm-Forming Staphylococcus aureus Isolates Belonging to USA300 and EMRSA-15 Clonal Lineages.

Sabirova, J S / Xavier, B B / Hernalsteens, J-P / De Greve, H / Ieven, M / Goossens, H / Malhotra-Kumar, S

Genome announcements

2014 Volume 2, Issue 3

Abstract: Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections that are even more difficult to treat when associated with a biofilm phenotype that facilitates evasion of the host immune system and antibiotics. As a first step toward ... ...

Abstract	Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections that are even more difficult to treat when associated with a biofilm phenotype that facilitates evasion of the host immune system and antibiotics. As a first step toward understanding the mechanisms underlying biofilm formation, we sequenced the genomes of two prolific biofilm-forming strains belonging to the two most important globally disseminated clonal lineages, USA300 and EMRSA-15.
Language	English
Publishing date	2014-06-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2704277-7
ISSN	2169-8287
ISSN	2169-8287
DOI	10.1128/genomeA.00610-14
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Article: Complete Genome Sequences of Two Prolific Biofilm-Forming Staphylococcus aureus Isolates Belonging to USA300 and EMRSA-15 Clonal Lineages

Sabirova, J. S / Xavier, B. B / Hernalsteens, J.-P / De Greve, H / Ieven, M / Goossens, H / Malhotra-Kumar, S

Genome announcements. 2014 June 26, v. 2, no. 3

2014

Abstract	Methicillin-resistant Staphylococcus aureus (MRSA) causes serious infections that are even more difficult to treat when associated with a biofilm phenotype that facilitates evasion of the host immune system and antibiotics. As a first step toward understanding the mechanisms underlying biofilm formation, we sequenced the genomes of two prolific biofilm-forming strains belonging to the two most important globally disseminated clonal lineages, USA300 and EMRSA-15.
Keywords	antibiotic resistance ; biofilm ; genome ; immune system ; methicillin ; methicillin-resistant Staphylococcus aureus ; nucleotide sequences ; phenotype
Language	English
Dates of publication	2014-0626
Size	p. e00610-14.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	2704277-7
ISSN	2169-8287
ISSN	2169-8287
DOI	10.1128/genomeA.00610-14
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Article ; Online: Fatty acid kinase A is an important determinant of biofilm formation in Staphylococcus aureus USA300.

Sabirova, J S / Hernalsteens, J-P / De Backer, S / Xavier, B B / Moons, P / Turlej-Rogacka, A / De Greve, H / Goossens, H / Malhotra-Kumar, S

BMC genomics

2015 Volume 16, Page(s) 861

Abstract: ... in a USA300 skin abscess isolate (UAS391) that formed prolific biofilms.: Methods: USA300 S. aureus strains ... comparison and functional genomics, identified fakA, a recently described fatty acid kinase in S. aureus ... virulence factors, as a negative regulator of biofilm formation in S. aureus USA300. ...

Abstract	Background: Methicillin-resistant Staphylococcus aureus (MRSA)-USA300 is notorious for its ability to cause community- and healthcare-acquired infections, which are even more difficult to treat when associated with a biofilm phenotype. We aimed to characterize the genetic determinants of biofilm formation in a USA300 skin abscess isolate (UAS391) that formed prolific biofilms. Methods: USA300 S. aureus strains, TCH1516 and FPR3757, were found to be closely related based on whole genome mapping (Argus™ Optical Mapping System, Opgen Inc, Gaithersburg, USA) to UAS391 (96.3-99.1 % similarity, P=0.0151), however differed markedly in biofilm formation (P=0.0001) on a dynamic assay (BioFlux 200, Fluxion Biosciences, USA). Comparison of whole genome sequences of these strains identified differences in a total of 18 genes. Corresponding Tn (bursa aurealis-bearing) knockout mutants in these target genes were obtained from a publicly available mutant library of the same clonal lineage (USA300-JE2) and were characterized phenotypically for biofilm formation. Tn mutants showing significant differences in biofilm formation were utilized for transduction into a plasmid-cured erythromycin-sensitive derivative of UAS391 and for complementation experiments. All strains were tested on the dynamic assay, and 17h-biofilms were stained (SYTO9, Life Technologies) and fluorescence intensity quantified by microscopy (Zeiss, ImageJ). Gene expression levels in Tn and transduced mutants were studied by quantitative reverse transcriptase PCR (StepOnePlusTM, Applied Biosystems®). Results: Comparison of the sequenced genomes of TCH1516, FPR3757 and UAS391 yielded a limited number of variant genes (n=18) that were hypothesized to account for the observed difference in biofilm-forming capacity. Screening of Tn mutants disrupted in these target genes identified one mutant (NE229) bearing a transposon insertion in SAUSA300_1119 (fakA), which exhibited increased biofilm formation similar to UAS391 (P=0.9320). Transduction experiments confirmed that fakA::Tn corresponded to 1.9- to 4.6-fold increase in biofilm formation depending on the USA300 strain background (P≤0.0007), while complementation of the TCH1516 wild-type fakA allele in UAS391 resulted in a 4.3-fold reduction in biofilm formation (P<0.0001). Conclusions: This sequential approach, consisting of strain typing, genome comparison and functional genomics, identified fakA, a recently described fatty acid kinase in S. aureus that is essential for phospholipid synthesis and also impacts the transcription of numerous virulence factors, as a negative regulator of biofilm formation in S. aureus USA300.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms/growth & development ; Genome, Bacterial/genetics ; Mutation ; Plasmids/genetics ; Staphylococcus aureus/enzymology ; Staphylococcus aureus/genetics ; Staphylococcus aureus/physiology
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2015-10-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-015-1956-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Employing whole genome mapping for optimal de novo assembly of bacterial genomes.

Xavier, Basil Britto / Sabirova, Julia / Pieter, Moons / Hernalsteens, Jean-Pierre / de Greve, Henri / Goossens, Herman / Malhotra-Kumar, Surbhi

BMC research notes

2014 Volume 7, Page(s) 484

Abstract: Background: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, ... ...

Abstract	Background: De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies. Findings: Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies. Conclusions: We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
MeSH term(s)	Chromosome Mapping/methods ; Contig Mapping ; Genome, Bacterial/genetics ; Sequence Analysis, DNA ; Software ; Staphylococcus aureus/genetics
Language	English
Publishing date	2014-07-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/1756-0500-7-484
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Article: Obtention and characterization of poly(3-hydroxybutyricacid-co-hydroxyvaleric acid)/mcI-PHA based blends

Martelli, S. M. / Sabirova, J. / Fakhoury, F. M. / Dyzma, A. / De Meyer, B. / Soetaert, W.

LWT - food science and technology

2012 Volume 47, Issue 2, Page(s) 386

Language	English
Document type	Article
ZDB-ID	2169058-3
ISSN	0023-6438
Database	Current Contents Nutrition, Environment, Agriculture

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Article ; Online: Roles of multiple acyl-CoA oxidases in the routing of carbon flow towards β-oxidation and polyhydroxyalkanoate biosynthesis in Yarrowia lipolytica.

Haddouche, Ramdane / Delessert, Syndie / Sabirova, Julia / Neuvéglise, Cécile / Poirier, Yves / Nicaud, Jean-Marc

FEMS yeast research

2010 Volume 10, Issue 7, Page(s) 917–927

Abstract: The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous ... ...

Abstract	The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous polyhydroxyalkanoate (PHA) synthase (phaC) of Pseudomonas aeruginosa in varying POX genetic backgrounds, thus allowing assessment of the impact of specific Aox enzymes on the routing of carbon flow to β-oxidation or to PHA biosynthesis. Analysis of PHA production yields during growth on fatty acids with different chain lengths has revealed that the POX genotype significantly affects the PHA levels, but not the monomer composition of PHA. Aox3p function was found to be responsible for 90% and 75% of the total PHA produced from either C9:0 or C13:0 fatty acid, respectively, whereas Aox5p encodes the main Aox involved in the biosynthesis of 70% of PHA from C9:0 fatty acid. Other Aoxs, such as Aox1p, Aox2p, Aox4p and Aox6p, were not found to play a significant role in PHA biosynthesis, independent of the chain length of the fatty acid used. Finally, three known models of β-oxidation are discussed and it is shown that a 'leaky-hose pipe model' of the cycle can be applied to Y. lipolytica.
MeSH term(s)	Acyl-CoA Oxidase/metabolism ; Acyltransferases/genetics ; Acyltransferases/metabolism ; Carbon/metabolism ; Fatty Acids/metabolism ; Oxidation-Reduction ; Polyhydroxyalkanoates/metabolism ; Pseudomonas aeruginosa/enzymology ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Yarrowia/enzymology ; Yarrowia/growth & development ; Yarrowia/metabolism
Chemical Substances	Fatty Acids ; Polyhydroxyalkanoates ; Recombinant Proteins ; Carbon (7440-44-0) ; Acyl-CoA Oxidase (EC 1.3.3.6) ; Acyltransferases (EC 2.3.-) ; poly(3-hydroxyalkanoic acid) synthase (EC 2.3.1.-)
Language	English
Publishing date	2010-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2036775-2
ISSN	1567-1364 ; 1567-1356
ISSN (online)	1567-1364
ISSN	1567-1356
DOI	10.1111/j.1567-1364.2010.00670.x
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Article ; Online: Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS.

Sabirova, Julia S / Xavier, Basil Britto / Coppens, Jasmine / Zarkotou, Olympia / Lammens, Christine / Janssens, Lore / Burggrave, Ronald / Wagner, Trevor / Goossens, Herman / Malhotra-Kumar, Surbhi

The Journal of antimicrobial chemotherapy

2016 Volume 71, Issue 6, Page(s) 1501–1509

Abstract: ... to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's ...

Abstract	Objectives: We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). Methods: All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). Results: All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212-0.849) (P = 0.007). Conclusions: This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.
MeSH term(s)	Bacterial Proteins/genetics ; Chromosome Mapping/methods ; Electrophoresis, Gel, Pulsed-Field ; Europe/epidemiology ; Genotype ; Humans ; Klebsiella Infections/epidemiology ; Klebsiella Infections/microbiology ; Klebsiella pneumoniae/classification ; Klebsiella pneumoniae/enzymology ; Klebsiella pneumoniae/genetics ; Klebsiella pneumoniae/isolation & purification ; Longitudinal Studies ; Molecular Epidemiology/methods ; Multilocus Sequence Typing/methods ; beta-Lactamases/genetics
Chemical Substances	Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; carbapenemase (EC 3.5.2.6)
Language	English
Publishing date	2016
Publishing country	England
Document type	Comparative Study ; Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkw003
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