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Article ; Online: A computational model revealing the immune-related hub genes and key pathways involved in rheumatoid arthritis (RA).

Balasundaram, Ambritha / Udhaya Kumar, S / George Priya Doss, C

Advances in protein chemistry and structural biology

2022 Volume 129, Page(s) 247–273

Abstract: ... performed and obtained the top two modules in each DEG's upregulated and downregulated protein-protein ...

Abstract	Rheumatoid arthritis (RA) has one of the highest disability rates among inflammatory joint disorders. However, the reason and possible molecular events are still unclear. There are various treatment options available, but no complete cure. To obtain early diagnosis and successful medication in RA, it is necessary to explore gene susceptibility and pathogenic factors. The main intend of our work is to explore the immune-related hub genes with similar functions that are differentially expressed in RA patients. Three datasets such as GSE21959, GSE55457, and GSE77298, were taken to analyze the differently expressed genes (DEGs) among 55 RA and 33 control samples. We obtained 331 upregulated and 275 downregulated DEGs from three Gene Expression Omnibus (GEO) datasets using the R package. Furthermore, a protein-protein interaction network was built for upregulated and downregulated DEGs using Cytoscape. Subsequently, MCODE analysis was performed and obtained the top two modules in each DEG's upregulated and downregulated protein-protein interactions (PPIs) network. CytoNCA and cytoHubba were performed and identified overlapping DEGs. In addition, we narrowed down DEGs by filtering with immune-related genes and identified DE-IRGs. Gene ontology (GO) and KEGG pathway analysis in upregulated and downregulated DEGs were executed with the DAVID platform. Our study obtained the nine most significant DE-IRGs in RA such as CXCR4, CDK1, BUB1, BIRC5, AGTR1, EGFR, EDNRB, KALRN, and GHSR. Among them, CXCR4, CDK1, BUB1, and BIRC5 are overexpressed in RA and may contribute to the pathophysiology of the disease. Similarly, AGTR1, EGFR, EDNRB, KALRN, and GHSR are all low expressed in RA and may have a contribution to pathogenesis. GO, KEGG functional enrichment, and GeneMANIA showed that the dysregulated process of DE-IRGs causes RA development and progression. These findings may be helpful in future studies in RA diagnosis and therapy.
MeSH term(s)	Arthritis, Rheumatoid/genetics ; Arthritis, Rheumatoid/metabolism ; Computational Biology ; Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; Protein Interaction Maps/genetics
Language	English
Publishing date	2022-02-08
Publishing country	Netherlands
Document type	Journal Article
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2021.11.006
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Article ; Online: Computational and structural investigation of Palmitoyl-Protein Thioesterase 1 (PPT1) protein causing Neuronal Ceroid Lipofuscinoses (NCL).

Thirumal Kumar, D / Shaikh, Nishaat / Udhaya Kumar, S / George Priya Doss, C

Advances in protein chemistry and structural biology

2022 Volume 132, Page(s) 89–109

Abstract: The Neuronal Ceroid Lipofuscinoses (NCL) are a group of progressive neurodegenerative disorders, associated with 14 Ceroid Lipofuscinosis Neuronal genes (CLN1-14). The mutations in the Palmitoyl-Protein Thioesterase 1 (PPT1) protein serve as one of the ... ...

Abstract	The Neuronal Ceroid Lipofuscinoses (NCL) are a group of progressive neurodegenerative disorders, associated with 14 Ceroid Lipofuscinosis Neuronal genes (CLN1-14). The mutations in the Palmitoyl-Protein Thioesterase 1 (PPT1) protein serve as one of the major reasons for the causative of NCL. The PPT1 involves degrading and modifying cysteine residues in proteins or peptides by removing thioester-linked fatty acyl groups like palmitate prefers acyl chains of 14-18 carbons in length. In this study, we have analyzed the impact of PPT1 mutations on the deleteriousness, stability, conservative nature of amino acid, and impact of mutations on the protein structure. We have also used molecular dynamics simulations using GROMACS to perceive the alteration in the dynamic behavior of the PPT1 at the residual level. In this study, we have retrieved 23 PPT1 mutations from the UniProt database, and these were subjected to a series of analyses using varied computer algorithms. From these analyses, out of 23 mutations, 16 mutations were identified as deleterious. Among 16, eight mutations were identified to destabilize the protein structure, and finally, two mutations (W38C and L222P) were found to be positioned in the highly conserved region. The structural impact study observed that the mutant proline could disrupt the alpha helix formed by the leucine at position 222. Finally, from the molecular dynamics simulations, we observed that due to the mutations (W38C and L222P), the protein had experienced higher deviation, fluctuation, and lower compactness. These structural changes elucidate that these mutations can impact the structure and function of the PPT1 protein.
MeSH term(s)	Humans ; Membrane Proteins/genetics ; Mutation ; Neuronal Ceroid-Lipofuscinoses/genetics ; Thiolester Hydrolases/chemistry ; Thiolester Hydrolases/genetics ; Thiolester Hydrolases/metabolism
Chemical Substances	Membrane Proteins ; Thiolester Hydrolases (EC 3.1.2.-) ; PPT1 protein, human (EC 3.1.2.22) ; palmitoyl-protein thioesterase (EC 3.1.2.22)
Language	English
Publishing date	2022-08-18
Publishing country	Netherlands
Document type	Journal Article
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2022.07.002
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Article ; Online: Molecular characterization of circadian gene expression and its correlation with survival percentage in colorectal cancer patients.

Datta, Ankur / R, Hephzibah Cathryn / Udhaya Kumar, S / Vasudevan, Karthick / Thirumal Kumar, D / Zayed, Hatem / George Priya Doss, C

Advances in protein chemistry and structural biology

2023 Volume 137, Page(s) 161–180

Abstract: Colorectal cancer (CRC) is a form of cancer characterized by many symptoms and readily metastasizes to different organs in the body. Circadian rhythm is one of the many processes that is observed to be dysregulated in CRC-affected patients. In this study, ...

Abstract	Colorectal cancer (CRC) is a form of cancer characterized by many symptoms and readily metastasizes to different organs in the body. Circadian rhythm is one of the many processes that is observed to be dysregulated in CRC-affected patients. In this study, we aim to identify the dysregulated physiological processes in CRC-affected patients and correlate the expression profiles of the circadian clock genes with CRC-patients' survival rates. We performed an extensive microarray gene expression pipeline, whereby 471 differentially expressed genes (DEGs) were identified, following which, we streamlined our search to 43 circadian clock affecting DEGs. The Circadian Gene Database was accessed to retrieve the circadian rhythm-specific genes. The DEGs were then subjected to multi-level functional annotation, i.e., preliminary analysis using ClueGO/CluePedia and pathway enrichment using DAVID. The findings of our study were interesting, wherein we observed that the survival percentage of CRC-affected patients dropped significantly around the 100th-month mark. Furthermore, we identified hormonal activity, xenobiotic metabolism, and PI3K-Akt signaling pathway to be frequently dysregulated cellular functions. Additionally, we detected that the ZFYVE family of genes and the two genes, namely MYC and CDK4 were the significant DEGs that are linked to the pathogenesis and progression of CRC. This study sheds light on the importance of bioinformatics to simplify our understanding of the interactions of different genes that control different phenotypes.
MeSH term(s)	Humans ; Phosphatidylinositol 3-Kinases ; Computational Biology ; Phenotype ; Colorectal Neoplasms/genetics ; Gene Expression
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-)
Language	English
Publishing date	2023-03-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2473077-4
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2023.02.007
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Article: Kerala, India's Front Runner in Novel Coronavirus Disease (COVID-19).

Udhaya Kumar, S / Thirumal Kumar, D / Siva, R / George Priya Doss, C

Frontiers in medicine

2020 Volume 7, Page(s) 355

Keywords	covid19
Language	English
Publishing date	2020-07-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2775999-4
ISSN	2296-858X
ISSN	2296-858X
DOI	10.3389/fmed.2020.00355
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Article ; Online: Identification of dysregulated canonical pathways associated with pathogenesis and progression of Amyotrophic Lateral Sclerosis-An integrated bioinformatics approach.

Datta, Ankur / Udhaya Kumar, S / D'costa, Maria / Bothe, Anusha / Thirumal Kumar, D / Zayed, Hatem / George Priya Doss, C

Advances in protein chemistry and structural biology

2023 Volume 134, Page(s) 21–52

Abstract: ... functional analysis using ClueGO/CluePedia plug-in. Qiagen's IPA software was employed for enrichment ...

Abstract	The mechanisms responsible for the pathogenesis and progression of Amyotrophic Lateral Sclerosis (ALS) remain poorly understood, making the diagnosis of ALS challenging. We aimed to find the novel gene biomarkers via computationally analyzing microarray expression studies, in three different cell lineages, namely myotube cells, astrocyte cells and oligodendrocyte cells. Microarray gene expression profiles were obtained and analyzed for three cell types: myotube cell lineage (GSE122261), astrocyte, and oligodendrocyte cell lineage (GSE87385). A comprehensive computational pipeline, tailored explicitly for microarray gene expression profiling studies, was devised to analyze the sample groups, wherein the myotube sample group comprised of six control (GSM3462697, GSM3462698, GSM3462699, GSM3462700, GSM3462701, GSM3462702) & six diseased (GSM3462691, GSM3462692, GSM3462693, GSM3462694, GSM3462695, GSM3462696) samples were considered. Similarly, for the astrocyte sample group two samples each for the control (GSM2330040, GSM2330042) and the diseased (GSM2330039, GSM2330041), and for the oligodendrocyte sample group, 2 control (GSM2330043, GSM2330045) samples and two diseased (GSM2330044, GSM2330046) samples were considered for the current study. The in-depth interaction of these DEGs was studied using MCODE and subjected to preliminary functional analysis using ClueGO/CluePedia plug-in. Qiagen's IPA software was employed for enrichment analysis, which generated the key canonical pathways and a list of potential biomarker molecules specific to each sample group. The preliminary analysis yielded 512 DEGs across all 3-sample groups, wherein 139 DEGs belonged to the myotube sample group, 216 DEGs for the astrocyte sample group, and 157 DEGs for the oligodendrocytes sample group. The data suggests growth hormone signaling and its activity, ErbB signaling pathway, and JAK/STAT signaling pathway are some of the pathways that are significantly dysregulated and play a crucial role in the development and progression of ALS. KISS1R and CSHL1 are potential genes that could act as diagnostic biomarkers in myotube cell types. Also, KRAS, TGFB2, JUN, and SMAD6 genes may be used as prognostic biomarkers to differentiate between early and late-stage ALS-diseased patients.
MeSH term(s)	Humans ; Amyotrophic Lateral Sclerosis/metabolism ; Computational Biology ; Gene Expression Profiling ; Signal Transduction
Language	English
Publishing date	2023-01-04
Publishing country	Netherlands
Document type	Journal Article
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2022.11.014
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Article ; Online: A review of bioinformatics tools and web servers in different microarray platforms used in cancer research.

Hephzibah Cathryn, R / Udhaya Kumar, S / Younes, Salma / Zayed, Hatem / George Priya Doss, C

Advances in protein chemistry and structural biology

2022 Volume 131, Page(s) 85–164

Abstract: Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work ... ...

Abstract	Over the past decade, conventional lab work strategies have gradually shifted from being limited to a laboratory setting towards a bioinformatics era to help manage and process the vast amounts of data generated by omics technologies. The present work outlines the latest contributions of bioinformatics in analyzing microarray data and their application to cancer. We dissect different microarray platforms and their use in gene expression in cancer models. We highlight how computational advances empowered the microarray technology in gene expression analysis. The study on protein-protein interaction databases classified into primary, derived, meta-database, and prediction databases describes the strategies to curate and predict novel interaction networks in silico. In addition, we summarize the areas of bioinformatics where neural graph networks are currently being used, such as protein functions, protein interaction prediction, and in silico drug discovery and development. We also discuss the role of deep learning as a potential tool in the prognosis, diagnosis, and treatment of cancer. Integrating these resources efficiently, practically, and ethically is likely to be the most challenging task for the healthcare industry over the next decade; however, we believe that it is achievable in the long term.
MeSH term(s)	Computational Biology ; Databases, Factual ; Drug Discovery ; Humans ; Neoplasms/diagnosis ; Neoplasms/genetics
Language	English
Publishing date	2022-06-17
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2022.05.002
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Article ; Online: CDK regulators-Cell cycle progression or apoptosis-Scenarios in normal cells and cancerous cells.

Nilmani / D'costa, Maria / Bothe, Anusha / Das, Soumik / Udhaya Kumar, S / Gnanasambandan, R / George Priya Doss, C

Advances in protein chemistry and structural biology

2023 Volume 135, Page(s) 125–177

Abstract: ... CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively ...

Abstract	Serine/threonine kinases called cyclin-dependent kinases (CDKs) interact with cyclins and CDK inhibitors (CKIs) to control the catalytic activity. CDKs are essential controllers of RNA transcription and cell cycle advancement. The ubiquitous overactivity of the cell cycle CDKs is caused by a number of genetic and epigenetic processes in human cancer, and their suppression can result in both cell cycle arrest and apoptosis. This review focused on CDKs, describing their kinase activity, their role in phosphorylation inhibition, and CDK inhibitory proteins (CIP/KIP, INK 4, RPIC). We next compared the role of different CDKs, mainly p21, p27, p57, p16, p15, p18, and p19, in the cell cycle and apoptosis in cancer cells with respect to normal cells. The current work also draws attention to the use of CDKIs as therapeutics, overcoming the pharmacokinetic barriers of pan-CDK inhibitors, analyze new chemical classes that are effective at attacking the CDKs that control the cell cycle (cdk4/6 or cdk2). It also discusses CDKI's drawbacks and its combination therapy against cancer patients. These findings collectively demonstrate the complexity of cancer cell cycles and the need for targeted therapeutic intervention. In order to slow the progression of the disease or enhance clinical outcomes, new medicines may be discovered by researching the relationship between cell death and cell proliferation.
MeSH term(s)	Humans ; Cell Cycle Proteins/genetics ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/pharmacology ; Cyclin-Dependent Kinases ; Cell Cycle ; Apoptosis
Chemical Substances	Cell Cycle Proteins ; Cyclin-Dependent Kinase Inhibitor p21 ; Cyclin-Dependent Kinases (EC 2.7.11.22)
Language	English
Publishing date	2023-02-06
Publishing country	Netherlands
Document type	Review ; Journal Article
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2022.11.008
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Article ; Online: Structure-based virtual screening to identify potential lipase inhibitors to reduce lipid storage in Wolman disorder.

Vasudevan, Karthick / Udhaya Kumar, S / Mithun, A / Raghavendra, B / George Priya Doss, C

Advances in protein chemistry and structural biology

2022 Volume 133, Page(s) 351–363

Abstract: Wolman disorder (WD) was first described in Iranian-Jewish (IJ) children, and it is caused by a deficiency of the lysosomal acid lipase (LAL). Newborns with WD are healthy and active at birth but soon develop severe malnutrition symptoms and often die ... ...

Abstract	Wolman disorder (WD) was first described in Iranian-Jewish (IJ) children, and it is caused by a deficiency of the lysosomal acid lipase (LAL). Newborns with WD are healthy and active at birth but soon develop severe malnutrition symptoms and often die before 1 year. In particular, spleens, livers, bone marrows, intestines, adrenal glands, and lymph nodes accumulate harmful amounts of lipids. G87V mutation in LIPA is responsible for Wolman disorder. Some reports suggest that δ-tocopherol can reduce lipid accumulation in cholesterol storage disorders. Hence, we used δ-tocopherol for the virtual screening process in this study. Initially, the lead compounds were docked with native and G87V mutant LIPA. Subsequently, the ADME and toxicity parameters for screened compounds were determined to ensure the safety profiles. Finally, the molecular dynamics simulations result indicated that dl-alpha-Tocopherol-13C3, a molecule obtained from the PubChem database, is identified as a potential and stable lead molecule that could be effective against the G87V mutant form of LIPA.
MeSH term(s)	Child ; Infant, Newborn ; Humans ; Wolman Disease/drug therapy ; Wolman Disease/genetics ; Iran ; Sterol Esterase/genetics ; Lipase/genetics ; Lipids
Chemical Substances	Sterol Esterase (EC 3.1.1.13) ; Lipase (EC 3.1.1.3) ; Lipids
Language	English
Publishing date	2022-11-30
Publishing country	Netherlands
Document type	Journal Article
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/bs.apcsb.2022.10.010
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Article ; Online: Gene network interaction analysis to elucidate the antimicrobial resistance mechanisms in the Clostridiumdifficile.

Anusha, M / Tejaswini, V / Udhaya Kumar, S / Prashantha, C N / Vasudevan, Karthick / George Priya Doss, C

Microbial pathogenesis

2023 Volume 178, Page(s) 106083

Abstract: Antimicrobial resistance has caused chaos worldwide due to the depiction of multidrug-resistant (MDR) infective microorganisms. A thorough examination of antimicrobial resistance (AMR) genes and associated resistant mechanisms is vital to solving this ... ...

Abstract	Antimicrobial resistance has caused chaos worldwide due to the depiction of multidrug-resistant (MDR) infective microorganisms. A thorough examination of antimicrobial resistance (AMR) genes and associated resistant mechanisms is vital to solving this problem. Clostridium difficile (C. difficile) is an opportunistic nosocomial bacterial strain that has acquired exogenous AMR genes that confer resistance to antimicrobials such as erythromycin, azithromycin, clarithromycin, rifampicin, moxifloxacin, fluoroquinolones, vancomycin, and others. A network of interactions, including 20 AMR genes, was created and analyzed. In functional enrichment analysis, Cellular components (CC), Molecular Functions (MF), and Biological Processes (BP) were discovered to have substantial involvement. Mutations in the rpl genes, which encode ribosomal proteins, confer resistance in Gram-positive bacteria. Full erythromycin and azithromycin cross-resistance can be conferred if more than one of the abovementioned genes is present. In the enriched BP, rps genes related to transcriptional regulation and biosynthesis were found. The genes belong to the rpoB gene family, which has previously been related to rifampicin resistance. The genes rpoB, gyrA, gyrB, rpoS, rpl genes, rps genes, and Van genes are thought to be the hub genes implicated in resistance in C. difficile. As a result, new medications could be developed using these genes. Overall, our observations provide a thorough understanding of C. difficile AMR mechanisms.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Clostridioides difficile/genetics ; Rifampin ; Azithromycin ; Gene Regulatory Networks ; Drug Resistance, Bacterial/genetics ; Anti-Infective Agents/pharmacology ; Erythromycin ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents ; Rifampin (VJT6J7R4TR) ; Azithromycin (83905-01-5) ; Anti-Infective Agents ; Erythromycin (63937KV33D)
Language	English
Publishing date	2023-03-22
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2023.106083
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Article ; Online: HPV and molecular mimicry in systemic lupus erythematosus and an impact of compiling B-cell epitopes and MHC-class II binding profiles with

Calvin, D John Dickson / Steve, Runal John / Kannangai, Rajesh / Abraham, Priya / Udhaya Kumar, S / Balasundaram, Ambritha / George Priya Doss, C / Thomas, Vinotha / Thomas, Anitha / Danda, Debashish / Fletcher, John Gnanadurai

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 21, Page(s) 12338–12346

Abstract: Epidemiological link between HPV and SLE is evolving. The possibility of HPV infection-induced molecular mimicry and systemic lupus erythematosus (SLE) was elucidated through ... ...

Abstract	Epidemiological link between HPV and SLE is evolving. The possibility of HPV infection-induced molecular mimicry and systemic lupus erythematosus (SLE) was elucidated through detailed
MeSH term(s)	Humans ; Epitopes, B-Lymphocyte ; Papillomavirus Infections ; Molecular Mimicry ; Molecular Docking Simulation ; Lupus Erythematosus, Systemic ; Peptides/chemistry ; Epitopes, T-Lymphocyte
Chemical Substances	Epitopes, B-Lymphocyte ; Peptides ; Epitopes, T-Lymphocyte
Language	English
Publishing date	2023-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2175261
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