@misc{SchierackHeidenKhanetal., author = {Schierack, Peter and Heiden, Stefan E. and Khan, Muhammad Moman and Nikolaus, Lena and Kolenda, Rafał and Stubbe, Michael and Lkhagvasuren, Davaa and R{\"o}diger, Stefan and Guenther, Sebastian and Schaufler, Katharina}, title = {Genomic and Phenotypic Analysis of an ESBL-Producing E. coli ST1159 Clonal Lineage From Wild Birds in Mongolia}, series = {Frontiers in Microbiology}, volume = {11}, journal = {Frontiers in Microbiology}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.01699}, pages = {7}, language = {en} } @misc{ReimannRoedigerSteinetal., author = {Reimann, Ronny and R{\"o}diger, Stefan and Stein, Erhard and Kilian, Andr{\`e} and Dittrich, Corinne and Petrick, Ingolf}, title = {Die Beschreibung der Fluiddynamik und der Lichtintensit{\"a}t im neuen MULT Reaktor}, publisher = {DECHEMA}, address = {Frankfurt, M.}, pages = {S. 30}, language = {de} } @misc{GeorgeRoedigerSchroederetal., author = {George, Sandra and R{\"o}diger, Stefan and Schr{\"o}der, Christian and Knaut, Michael and K{\"u}pper, Jan-Heiner}, title = {Development of multiplex PCR systems for expression profiling of human cardiomyocytes induced to profilerate by lentivirus transduction of upcyte genes}, series = {Journal of Cellular Biotechnology}, volume = {2}, journal = {Journal of Cellular Biotechnology}, number = {1}, issn = {2352-3697}, doi = {10.3233/JCB-15025}, pages = {35 -- 55}, language = {en} } @misc{GrunerMoncsekRoedigeretal., author = {Gruner, Melanie and Moncsek, Anja and R{\"o}diger, Stefan and K{\"u}hnhardt, Dagmar and Feist, Eugen and Stohwasser, Ralf}, title = {Increased proteasome activator 28 gamma (PA28g) levels are unspecific but correlate with disease activity in rheumatoid arthritis}, series = {BMC musculoskeletal disorders}, volume = {15}, journal = {BMC musculoskeletal disorders}, issn = {1471-2474}, doi = {10.1186/1471-2474-15-414}, pages = {414 -- 424}, language = {en} } @misc{WillitzkiHiemannPetersetal., author = {Willitzki, Annika and Hiemann, Rico and Peters, Vanessa and Sack, Ulrich and Schierack, Peter and R{\"o}diger, Stefan and Anderer, Ursula and Conrad, Karsten and Bogdanos, Dimitrios Petrou and Reinhold, Dirk and Roggenbuck, Dirk}, title = {New PlatformTechnology for Comprehensive Serological Diagnostics of Autoimmune Diseases}, series = {Clinical and Developmental Immunology}, journal = {Clinical and Developmental Immunology}, issn = {1740-2530}, doi = {10.1155/2012/284740}, pages = {1 -- 8}, language = {en} } @misc{KundzerVolkovaBogdanosetal., author = {Kundzer, Alena V. and Volkova, Margarita V. and Bogdanos, Dimitrios Petrou and R{\"o}diger, Stefan and Schierack, Peter and Generalov, I. and Nevinsky, G. A. and Roggenbuck, Dirk}, title = {Deoxyribonuclease activity of polyclonal IgGs: a putative serological marker in patients with spondyloarthritides}, series = {Immunologic Research}, volume = {56}, journal = {Immunologic Research}, number = {2-3}, issn = {0257-277X}, doi = {10.1007/s12026-013-8424-9}, pages = {457 -- 464}, abstract = {Antibodies executing catalytic activity are referred to as antibody enzymes or short "abzymes" and may have diagnostic relevance. Abzymes with deoxyribonuclease (DNase) activity have been demonstrated in patients with autoimmune and infectious diseases. Despite several reports on the occurrence of DNase abzymes in systemic autoimmune rheumatic diseases, conclusive data about DNase activity of antibodies in patients with spondyloarthritides (SpAs) are lacking. In recent cross-sectional studies evaluating levels of IgG DNase activity in patients with psoriatic arthritis (PsA), reactive arthritis (ReA), and ankylosing spondylitis (AS), DNase activity of IgG has been assessed by the rivanol clot method and confirmed by agarose gel electrophoresis. Remarkably, levels of IgG DNase activity were significantly higher in sera of SpA patients than those in control subjects. In patients with PsA, ReA, and AS, a positive correlation of DNase IgG activity with synovitis, disease activity, and stage of spondylitis was observed, respectively. Given the involvement of autoimmune reactions in cytolysis and connective tissue degradation in PsA, ReA, and to a lesser extent in AS, abzymes might have an impact on the pathophysiology of SpAs. Detection of IgG DNase activity in patients suffering from SpA represents an exciting new research field and may assist in the differential diagnosis of SpA.}, language = {en} } @misc{SchierackRoedigerKuhletal., author = {Schierack, Peter and R{\"o}diger, Stefan and Kuhl, Christoph and Hiemann, Rico and Roggenbuck, Dirk and Li, Ganwu and Weinreich, J{\"o}rg and Berger, Enrico and Nolan, Lisa K. and Nicholson, Bryon and R{\"o}mer, Antje and Fr{\"o}mmel, Ulrike and Wieler, Lothar H. and Schr{\"o}der, Christian}, title = {Porcine E. coli: Virulence-Associated Genes, Resistance Genes and Adhesion and Probiotic Activity Tested by a New Screening Method}, series = {PLoS One}, volume = {8}, journal = {PLoS One}, number = {4}, doi = {10.1371/journal.pone.0059242}, pages = {13}, abstract = {We established an automated screening method to characterize adhesion of Escherichia coli to intestinal porcine epithelial cells (IPEC-J2) and their probiotic activity against infection by enteropathogenic E. coli (EPEC). 104 intestinal E. coli isolates from domestic pigs were tested by PCR for the occurrence of virulence-associated genes, genes coding for resistances to antimicrobial agents and metals, and for phylogenetic origin by PCR. Adhesion rates and probiotic activity were examined for correlation with the presence of these genes. Finally, data were compared with those from 93 E. coli isolates from wild boars. Isolates from domestic pigs carried a broad variety of all tested genes and showed great diversity in gene patterns. Adhesions varied with a maximum of 18.3 or 24.2 mean bacteria adherence per epithelial cell after 2 or 6 hours respectively. Most isolates from domestic pigs and wild boars showed low adherence, with no correlation between adhesion/probiotic activity and E. coli genes or gene clusters. The gene sfa/foc, encoding for a subunit of F1C fimbriae did show a positive correlative association with adherence and probiotic activity; however E. coli isolates from wild boars with the sfa/foc gene showed less adhesion and probiotic activity than E. coli with the sfa/foc gene isolated from domestic pigs after 6 hour incubation. In conclusion, screening porcine E. coli for virulence associated genes genes, adhesion to intestinal epithelial cells, and probiotic activity revealed a single important adhesion factor, several probiotic candidates, and showed important differences between E. coli of domestic pigs and wild boars.}, language = {en} } @misc{FroemmelLehmannRoedigeretal., author = {Fr{\"o}mmel, Ulrike and Lehmann, Werner and R{\"o}diger, Stefan and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Weinreich, J{\"o}rg and Groß, Julia and Roggenbuck, Dirk and Zinke, Olaf and Ansorge, Hermann and Vogel, Steffen and Klemm, Per and Wex, Thomas and Schr{\"o}der, Christian and Wieler, Lothar H. and Schierack, Peter}, title = {Adhesion of human and animal Escherichia coli strains in association with their virulence-associated genes and phylogenetic origins}, series = {Applied and environmental microbiology}, volume = {79}, journal = {Applied and environmental microbiology}, number = {19}, issn = {1098-5336}, doi = {10.1128/AEM.01384-13}, pages = {5814 -- 5829}, abstract = {Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.}, language = {en} } @misc{FroemmelBoehmNitschkeetal., author = {Fr{\"o}mmel, Ulrike and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Weinreich, J{\"o}rg and Groß, Julia and R{\"o}diger, Stefan and Wex, Thomas and Ansorge, Hermann and Zinke, Olaf and Schr{\"o}der, Christian and Roggenbuck, Dirk and Schierack, Peter}, title = {Adhesion patterns of commensal and pathogenic Escherichia coli from humans and wild animals on human and porcine epithelial cell lines}, series = {Gut Pathogens}, volume = {5}, journal = {Gut Pathogens}, number = {31}, issn = {1757-4749}, doi = {10.1186/1757-4749-5-31}, pages = {8}, abstract = {Abstract BACKGROUND: Different strategies of colonization or infection by E. coli result in formation of certain adhesion patterns which help also in classifying intestinal E. coli into pathotypes. Little is known about adhesion patterns and host- and tissue adaption of commensal E. coli and about E. coli originating in clinically healthy hosts carrying pathotype-specific virulence-associated genes. FINDINGS: Adhesion pattern of E. coli (n = 282) from humans and from 18 animal species were verified on intestinal human Caco-2 and porcine IPEC-J2 cells and, furthermore, for comparison on human urinary bladder 5637, porcine kidney PK-15 epithelial and HEp-2 cells. The analysis was carried out on 150,000 images of adhesion assays.Adhesion patterns were very diverse; 88 isolates were completely non-adherent, whereas 194 adhered to at least one cell line with the dominant adhesion patterns "diffusely distributed" and "microcolony formation". Adhesion patterns "chains" and "clumps" were also visible. Chain formation was mediated by the presence of epithelial cells. Clump formation was very specific on only the 5637 cell line. All enteropathogenic (eae+) E. coli (EPEC; n = 14) were able to form microcolonies which was cell line specific for each isolate. Most EPEC formed microcolonies on intestinal IPEC-J2 and Caco-2 but several also on urinary tract cells. Shigatoxin-producing (stx+) E. coli (n = 10) showed no specific adhesion patterns. CONCLUSIONS: E. coli isolates were highly diverse. Commensal and pathogenic isolates can adhere in various forms, including diffuse distribution, microcolonies, chains and clumps. Microcolony formation seems to be a global adhesion strategy also for commensal E. coli.}, language = {en} } @misc{RoedigerRuhlandSchroederetal., author = {R{\"o}diger, Stefan and Ruhland, Mirko and Schr{\"o}der, Christian and Großmann, Kai and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Berger, Ingo and Schimke, Ingolf and Schierack, Peter}, title = {Fluorescence dye adsorption assay to quantify carboxyl groups on the surface of poly(methyl methacrylate) microbeads}, series = {Analytical Chemistry}, volume = {83}, journal = {Analytical Chemistry}, number = {9}, issn = {0003-2700}, doi = {10.1021/ac103277s}, pages = {3379 -- 3385}, language = {en} } @incollection{RoedigerSchierackBoehmetal., author = {R{\"o}diger, Stefan and Schierack, Peter and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Berger, Ingo and Fr{\"o}mmel, Ulrike and Schmidt, Carsten and Ruhland, Mirko and Schimke, Ingolf and Roggenbuck, Dirk and Lehmann, Werner and Schr{\"o}der, Christian}, title = {A highly versatile microscope imaging technology platform for the multiplex real-time detection of biomolecules and autoimmune antibodies}, series = {Molecular diagnostics}, booktitle = {Molecular diagnostics}, editor = {Seitz, Harald and Berger, Ingo}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-37690-0}, pages = {35 -- 74}, language = {en} } @misc{KolendaBurdukiewiczSchiebeletal., author = {Kolenda, Rafał and Burdukiewicz, Michał and Schiebel, Juliane and R{\"o}diger, Stefan and Sauer, Lysann and Szabo, Istvan and Orlowska, Aleksandra and Weinreich, J{\"o}rg and Nitschke, J{\"o}rg and B{\"o}hm, Alexander and Gerber, Ulrike and Roggenbuck, Dirk and Schierack, Peter}, title = {Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation}, series = {Frontiers in Microbiology}, volume = {9}, journal = {Frontiers in Microbiology}, number = {1905}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.01905}, pages = {15}, language = {en} } @misc{RoedigerLiebschSchmidtetal., author = {R{\"o}diger, Stefan and Liebsch, Claudia and Schmidt, Carsten and Lehmann, Werner and Resch-Genger, U. and Schedler, Uwe and Schierack, Peter}, title = {Nucleic acid detection based on the use of microbeads: a review}, series = {Microchimica Acta}, volume = {181}, journal = {Microchimica Acta}, number = {11-12}, issn = {0026-3672}, doi = {10.1007/s00604-014-1243-4}, pages = {1151 -- 1168}, language = {en} } @misc{MirskyRoedigerSchieracketal., author = {Mirsky, Vladimir M. and R{\"o}diger, Stefan and Schierack, Peter and Roggenbuck, Dirk}, title = {Preface to the Special Issue on PCR on chip and related technologies}, series = {Microchimica Acta}, volume = {181}, journal = {Microchimica Acta}, number = {13/14}, doi = {10.1007/s00604-014-1246-1}, pages = {1609 -- 1610}, language = {en} } @misc{SowaGrossmannScholzetal., author = {Sowa, Mandy and Großmann, Kai and Scholz, Juliane and R{\"o}ber, Nadja and R{\"o}diger, Stefan and Schierack, Peter and Conrad, Karsten and Roggenbuck, Dirk and Hiemann, Rico}, title = {Der CytoBead-Assay - Eine neue M{\"o}glichkeit der multiparametrischen Autoantik{\"o}rperanalytik bei systemischen Autoimmunerkrankungen}, series = {Journal of Laboratory Medicine}, volume = {38}, journal = {Journal of Laboratory Medicine}, number = {6}, doi = {10.1515/labmed-2014-0041}, pages = {309 -- 317}, language = {de} } @misc{SchierackRoedigerKolendaetal., author = {Schierack, Peter and R{\"o}diger, Stefan and Kolenda, Rafał and Hiemann, Rico and Berger, Enrico and Grzymajlo, Krzysztof and Swidsinski, Alexander and Juretzek, Thomas and Meissner, Dirk and Mydlak, Karsten and Reinhold, Dirk and Nolan, Lisa K. and Roggenbuck, Dirk}, title = {Species-specific and pathotype-specific binding of bacteria to zymogen granule membrane glycoprotein 2 (GP2)}, series = {Gut}, volume = {64}, journal = {Gut}, number = {3}, issn = {1468-3288}, doi = {10.1136/gutjnl-2014-307854}, pages = {517 -- 519}, language = {en} } @misc{ScholzGrossmannKnuetteretal., author = {Scholz, Juliane and Großmann, Kai and Kn{\"u}tter, Ilka and Hiemann, Rico and Sowa, Mandy and R{\"o}ber, Nadja and R{\"o}diger, Stefan and Schierack, Peter and Reinhold, Dirk and Bogdanos, Dimitrios Petrou and Meroni, Pier Luigi and Radice, Antonella and Conrad, Karsten and Roggenbuck, Dirk}, title = {Second generation analysis of antinuclear antibody (ANA) by combination of screening and confirmatory testing}, series = {Clinical Chemistry and Laboratory Medicine}, volume = {53}, journal = {Clinical Chemistry and Laboratory Medicine}, number = {12}, issn = {1437-4331}, doi = {10.1515/cclm-2015-0083}, pages = {1991 -- 2002}, language = {en} } @misc{SchmidtRoedigerGruneretal., author = {Schmidt, Carsten and R{\"o}diger, Stefan and Gruner, Melanie and Moncsek, Anja and Stohwasser, Ralf and Hanack, Katja and Schierack, Peter and Schr{\"o}der, Christian}, title = {Multiplex localization of sequential peptide epitopes by use of a planar microbead chip}, series = {Analytica Chimica Acta}, volume = {908}, journal = {Analytica Chimica Acta}, issn = {0003-2670}, doi = {10.1016/j.aca.2015.12.030}, pages = {150 -- 160}, language = {en} } @misc{GrossmannRoeberHiemannetal., author = {Großmann, Kai and R{\"o}ber, Nadja and Hiemann, Rico and R{\"o}diger, Stefan and Schierack, Peter and Reinhold, Dirk and Laass, Martin W. and Conrad, Karsten and Roggenbuck, Dirk}, title = {Simultaneous detection of celiac disease-specific IgA antibodies and total IgA}, series = {Autoimmunity Highlights}, volume = {7}, journal = {Autoimmunity Highlights}, number = {2}, issn = {2038-0305}, doi = {10.1007/s13317-016-0073-2}, pages = {10}, language = {en} } @misc{BurdukiewiczRoedigerSobczyketal., author = {Burdukiewicz, Michał and R{\"o}diger, Stefan and Sobczyk, Piotr and Menschikowski, Mario and Schierack, Peter and Mackiewicz, Pawel}, title = {Methods for comparing multiple digital PCR experiments}, series = {Biomolecular Detection and Quantification}, volume = {9}, journal = {Biomolecular Detection and Quantification}, issn = {2214-7535}, doi = {10.1016/j.bdq.2016.06.004}, pages = {14 -- 19}, language = {en} } @misc{RoedigerKramerFroemmeletal., author = {R{\"o}diger, Stefan and Kramer, Toni and Fr{\"o}mmel, Ulrike and Weinreich, J{\"o}rg and Roggenbuck, Dirk and Guenther, Sebastian and Schaufler, Katharina and Schr{\"o}der, Christian and Schierack, Peter}, title = {Intestinal Escherichia coli colonization in a mallard duck population over four consecutive winter season}, series = {Environmental Microbiology}, volume = {17}, journal = {Environmental Microbiology}, number = {9}, issn = {1462-2920}, doi = {10.1111/1462-2920.12807}, pages = {3352 -- 3361}, language = {en} } @misc{RoedigerBurdukiewiczBlagodatskikhetal., author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Blagodatskikh, Konstantin A. and Jahn, Michael and Schierack, Peter}, title = {R as an Environment for the Reproducible Analysis of DNA Amplification Experiments}, series = {The R journal}, volume = {7}, journal = {The R journal}, number = {1}, issn = {2073-4859}, pages = {127 -- 150}, language = {en} } @misc{RoedigerBurdukiewiczSchierack, author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Schierack, Peter}, title = {chipPCR: an R package to pre-process raw data of amplification curves. Bioinformatics}, series = {Bioinformatics}, volume = {31}, journal = {Bioinformatics}, number = {17}, issn = {1367-4803}, doi = {10.1093/bioinformatics/btv205}, pages = {2900 -- 2902}, language = {en} } @inproceedings{RoedigerBoehmNitschkeetal., author = {R{\"o}diger, Stefan and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Stavitskaya, Luba and Gruner, Melanie and Kundzer, Alena V. and Volkova, Margarita V. and Generalov, I. and Schmidt, Carsten and Schr{\"o}der, Christian and Roggenbuck, Dirk and Schierack, Peter}, title = {Development of a Method for Multiplex Real-Time Analysis of Enzymatic Activity on a Microbead-Chip}, series = {Infection, tumors and autoimmunity, report on the 11th Dresden Symposium on Autoantibodies held in Dresden on September 1-4, 2013}, booktitle = {Infection, tumors and autoimmunity, report on the 11th Dresden Symposium on Autoantibodies held in Dresden on September 1-4, 2013}, publisher = {Pabst Science Publ.}, address = {Lengerich [u.a.]}, isbn = {978-3-89967-881-9}, pages = {275 -- 280}, language = {en} } @misc{RoedigerLehmannFroemmeletal., author = {R{\"o}diger, Stefan and Lehmann, Werner and Fr{\"o}mmel, Ulrike and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Burdukiewicz, Michał and Schr{\"o}der, Christian and Dangla, R{\´e}mi and Droniou, Magali and Schierack, Peter}, title = {The Modi Operandi of the VideoScan Platform for the Detection and Analysis of Nucleic Acids. Life Science Day 2013 \& 17. Leibniz Conference of Advanced Science, Freie Universit{\"a}t Berlin, 24.10.2013}, pages = {1}, language = {en} } @inproceedings{RoedigerBurdukiewicz, author = {R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {Reproducible Analysis of DNA Amplification Experiments with an Open Source Software Environment}, series = {Abstractbook, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, M{\"u}nster}, booktitle = {Abstractbook, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, M{\"u}nster}, language = {en} } @misc{KramerSchiebelZelcketal., author = {Kramer, Toni and Schiebel, Juliane and Zelck, Claudia and Weinreich, J{\"o}rg and Schierack, Peter and R{\"o}diger, Stefan}, title = {Genotyping and gene expression analysis of putative reference genes in Enterobacteriaceae, 67th Annual Meeting of the German Society of Hygiene and Microbiology (DGHM), 27.-30.09.2015, M{\"u}nster}, doi = {10.7490/f1000research.1111354.1}, language = {en} } @inproceedings{RoedigerBurdukiewiczHeiserichetal., author = {R{\"o}diger, Stefan and Burdukiewicz, Michał and Heiserich, Lisa and Schierack, Peter and Roggenbuck, Dirk}, title = {Digital Enumeration of Double Strand Breaks via γH2AX and Aassociated biomarkers in a Computing Environment for Reproducible Research}, series = {From autoantibody research to standardized diagnostic assays in the management of human diseases, report on the 12th Dresden Symposium on Autoantibodies, September 23-26, 2015}, booktitle = {From autoantibody research to standardized diagnostic assays in the management of human diseases, report on the 12th Dresden Symposium on Autoantibodies, September 23-26, 2015}, publisher = {Pabst Science Publishers}, address = {Lengerich}, isbn = {978-3-95853-104-8}, pages = {S. 413}, language = {en} } @misc{RoedigerSchneiderSaueretal., author = {R{\"o}diger, Stefan and Schneider, Jens and Sauer, Lysann and Reddig, Annika and Schierack, Peter and Roggenbuck, Dirk and Schr{\"o}der, Christian}, title = {A Multiparameter Platform for The Analysis of DNA Double-strand Breaks and Associated Biomarkers after genome Editing Austrian Biomarker Symposium (ASBD) 2016, 10.-11.03.2016, Wien, {\"O}sterreich}, language = {en} } @misc{SauerRoedigerSchneideretal., author = {Sauer, Lysann and R{\"o}diger, Stefan and Schneider, Jens and Schierack, Peter and Roggenbuck, Dirk and Schr{\"o}der, Christian}, title = {Functional Multiparameter Analy sis of Double-Strand Breaks and Associate Biomarkers during Genome Editing, Genome Editing and Gene Modulation Congress 2016, 6.-8.04.2016, Oxford, United Kingdom}, language = {en} } @misc{DeutschmannDinterRoedigeretal., author = {Deutschmann, Claudia and Dinter, Franziska and R{\"o}diger, Stefan and Roggenbuck, Dirk and Schierack, Peter}, title = {Comparison of Lab and Point of Care (POC) technologies - case study for CHI3L1, Potsdam Days on Bioanalysis}, pages = {1}, language = {en} } @inproceedings{RoedigerBoehmNitschkeetal., author = {R{\"o}diger, Stefan and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Stavitskaya, Luba and Gruner, Melanie and Kundzer, Alena V. and Volkova, Margarita V. and Generalov, I. and Schmidt, Carsten and Schr{\"o}der, Christian and Roggenbuck, Dirk and Schierack, Peter}, title = {Development of a Method for Multiplex Real-Time Analysis of Enzymati c Activity on a Microbead-Chip.}, series = {Infections, Tumors and Autoimmunity, Report on the 11th Dresden Symposium on Autoantibodies held in Dresden on September 01. - 04., 2013}, booktitle = {Infections, Tumors and Autoimmunity, Report on the 11th Dresden Symposium on Autoantibodies held in Dresden on September 01. - 04., 2013}, publisher = {Pabst Science Publ.}, address = {Lengerich}, isbn = {978-3-89967-881-9}, pages = {280}, language = {en} } @inproceedings{RoedigerHanschmannSteidleetal., author = {R{\"o}diger, Stefan and Hanschmann, Henning and Steidle, Michael and Schr{\"o}der, Christian and Schierack, Peter and Lehmann, Werner}, title = {Detection of Borrelia, Bordetella and HPV with the LoopTag Real-Time PCR Probe System}, series = {International journal of medical microbiology}, volume = {303}, booktitle = {International journal of medical microbiology}, number = {Supplement 1}, issn = {1618-0607}, pages = {12 -- 13}, language = {en} } @inproceedings{Roediger, author = {R{\"o}diger, Stefan}, title = {Applications of a Multipurpose Platf orm for the Detection and Analysis of Biomolecules}, series = {BioSensor, 9. Deutsches BioSensor Symposium, 11.-13. M{\"a}rz 2015}, booktitle = {BioSensor, 9. Deutsches BioSensor Symposium, 11.-13. M{\"a}rz 2015}, publisher = {M{\"u}nchen}, language = {en} } @misc{SpiessRoedigerBurdukiewiczetal., author = {Spiess, Andrej-Nikolai and R{\"o}diger, Stefan and Burdukiewicz, Michał and Volksdorf, Thomas and Tellinghuisen, Joel}, title = {System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation}, series = {Scientific Reports}, volume = {6}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/srep38951}, pages = {10}, language = {en} } @misc{BurdukiewiczSobczykRoedigeretal., author = {Burdukiewicz, Michał and Sobczyk, Piotr and R{\"o}diger, Stefan and Duda-Madej, Anna and Mackiewicz, Pawel and Kotulska, Malgorzata}, title = {Amyloidogenic motifs revealed by n-gram analysis}, series = {Scientific Reports}, volume = {7}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/s41598-017-13210-9}, pages = {12}, language = {en} } @misc{RoedigerLiefoldRuheetal., author = {R{\"o}diger, Stefan and Liefold, Marius and Ruhe, Madeleine and Reinwald, Mark and Beck, Eberhard and Deckert, P. Markus}, title = {Quantification of DNA double-strand breaks in peripheral blood mononuclear cells from healthy donors exposed to bendamustine by an automated H2AX assay- an exploratory study}, series = {Journal of Laboratory and Precision Medicine}, volume = {3}, journal = {Journal of Laboratory and Precision Medicine}, number = {47}, issn = {2519-9005}, doi = {10.21037/jlpm.2018.04.10}, pages = {12}, language = {en} } @misc{DinterDeutschmannSchieracketal., author = {Dinter, Franziska and Deutschmann, Claudia and Schierack, Peter and Dame, Gregory and R{\"o}diger, Stefan}, title = {Integration of Cardiovascular Disease Biomarkers in a Microfluidic Microbead Chip}, pages = {1}, language = {en} } @misc{SchiebelBoehmNitschkeetal., author = {Schiebel, Juliane and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Burdukiewicz, Michał and Weinreich, J{\"o}rg and Ali, Aamir and Roggenbuck, Dirk and R{\"o}diger, Stefan and Schierack, Peter}, title = {Genotypic and phenotypic characteristics in association with biofilm formation in different pathotypes of human clinical Escherichia coli isolates}, series = {Applied and Environmental Microbiology}, volume = {83}, journal = {Applied and Environmental Microbiology}, number = {24}, issn = {1098-5336}, doi = {10.1128/AEM.01660-17}, language = {en} } @misc{LiebschRoedigerBoehmetal., author = {Liebsch, Claudia and R{\"o}diger, Stefan and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Weinreich, J{\"o}rg and Fruth, Angelika and Roggenbuck, Dirk and Lehmann, Werner and Schedler, Uwe and Juretzek, Thomas and Schierack, Peter}, title = {Solid-phase microbead array for multiplex O-serotyping of Escherichia coli}, series = {Microchimica Acta}, volume = {184}, journal = {Microchimica Acta}, number = {5}, issn = {0026-3672}, doi = {10.1007/s00604-017-2088-4}, pages = {1405 -- 1415}, language = {en} } @misc{BurdukiewiczSpiessBlagodatskikhetal., author = {Burdukiewicz, Michał and Spiess, Andrej-Nikolai and Blagodatskikh, Konstantin A. and Lehmann, Werner and Schierack, Peter and R{\"o}diger, Stefan}, title = {Algorithms for automated detection of hook effect-bearing amplification curves}, series = {Biomolecular Detection and Quantification}, volume = {16}, journal = {Biomolecular Detection and Quantification}, issn = {2214-7535}, doi = {10.1016/j.bdq.2018.08.001}, pages = {1 -- 4}, language = {en} } @misc{ReddigRuebeRoedigeretal., author = {Reddig, Annika and R{\"u}be, Claudia E. and R{\"o}diger, Stefan and Schierack, Peter and Reinhold, Dirk and Roggenbuck, Dirk}, title = {DNA damage assessment and potential applications in laboratory diagnostics and precision medicine}, series = {Journal of Laboratory and Precision Medicine}, volume = {3}, journal = {Journal of Laboratory and Precision Medicine}, issn = {2519-9005}, doi = {10.21037/jlpm.2018.03.06}, pages = {15}, language = {en} } @misc{SchneiderWeissRuheetal., author = {Schneider, Jens and Weiss, Romano and Ruhe, Madeleine and Jung, Tobias and Roggenbuck, Dirk and Stohwasser, Ralf and Schierack, Peter and R{\"o}diger, Stefan}, title = {Open source bioimage informatic tools for the analysis of DNA damage and associated biomarkers}, series = {Journal of Laboratory and Precision Medicine}, volume = {4}, journal = {Journal of Laboratory and Precision Medicine}, issn = {2519-9005}, doi = {10.21037/jlpm.2019.04.05}, language = {en} } @misc{RuheRabeJurischkaetal., author = {Ruhe, Madeleine and Rabe, Dominik and Jurischka, Christoph and Schr{\"o}der, Julia and Schierack, Peter and Deckert, P. Markus and R{\"o}diger, Stefan}, title = {Molecular biomarkers of DNA damage in diffuse large-cell lymphoma-a review}, series = {Journal of Laboratory and Precision Medicine}, volume = {4}, journal = {Journal of Laboratory and Precision Medicine}, issn = {2519-9005}, doi = {10.21037/jlpm.2019.01.01}, pages = {20}, language = {en} } @misc{OloweAdefioyeAjayeobaetal., author = {Olowe, Olugbenga Adekunle and Adefioye, Olusolabomi J. and Ajayeoba, T. A. and Schiebel, Juliane and Weinreich, J{\"o}rg and Ali, Aamir and Burdukiewicz, Michał and R{\"o}diger, Stefan and Schierack, Peter}, title = {Phylogenetic grouping and biofilm formation of Multidrug Resistant Escherichia coli Isolates from Humans, Animals and Food products in South-west Nigeria}, series = {Scientific African}, volume = {6}, journal = {Scientific African}, issn = {2468-2276}, doi = {10.1016/j.sciaf.2019.e00158}, pages = {11}, language = {en} } @misc{ChoiSchmidtTinnefeldetal., author = {Choi, Youngeun and Schmidt, Carsten and Tinnefeld, Philip and Bald, Ilko and R{\"o}diger, Stefan}, title = {A new reporter design based on DNA origami nanostructures for quantification of short oligonucleotides using microbeads}, series = {Scientific Reports}, journal = {Scientific Reports}, number = {9}, issn = {2045-2322}, doi = {10.1038/s41598-019-41136-x.}, language = {en} } @misc{HerrmannRoedigerSchmidtetal., author = {Herrmann, Anna and R{\"o}diger, Stefan and Schmidt, Carsten and Schierack, Peter and Schedler, Uwe}, title = {Spatial Separation of Microbeads into Detection Levels by a Bioorthogonal Porous Hydrogel for Size-Selective Analysis und Increased Multiplexicity}, series = {Analytical chemistry}, volume = {91}, journal = {Analytical chemistry}, number = {13}, issn = {1520-6882}, doi = {10.1021/acs.analchem.9b01586.}, pages = {8484 -- 8491}, language = {en} } @misc{DinterBurdukiewiczSchieracketal., author = {Dinter, Franziska and Burdukiewicz, Michał and Schierack, Peter and Lehmann, Werner and Nestler, J{\"o}rg and Dame, Gregory and R{\"o}diger, Stefan}, title = {Simultaneous detection and quantification of DNA and protein biomarkers in spectrum of cardiovascular diseases in a microfluidic microbead chip}, series = {Analytical and Bioanalytical Chemistry}, volume = {411}, journal = {Analytical and Bioanalytical Chemistry}, number = {29}, issn = {1618-2650}, doi = {10.1007/s00216-019-02199-x}, pages = {7725 -- 7735}, language = {en} } @misc{DeutschmannSowaMurugaiyanetal., author = {Deutschmann, Claudia and Sowa, Mandy and Murugaiyan, Jayaseelan and Roessler, Uwe and R{\"o}ber, Nadja and Conrad, Karsten and Laass, Martin W. and Bogdanos, Dimitrios Petrou and Sipeki, Nora and Papp, Maria and R{\"o}diger, Stefan and Roggenbuck, Dirk and Schierack, Peter}, title = {Identification of Chitinase-3-Like Protein 1 as a Novel Neutrophil Antigenic Target in Crohn's Disease}, series = {Journal of Crohn's and Colitis}, volume = {13}, journal = {Journal of Crohn's and Colitis}, number = {7}, issn = {1876-4479}, doi = {10.1093/ecco-jcc/jjz012}, pages = {894 -- 904}, abstract = {Background and Aims There is an increasing incidence of inflammatory bowel disease [IBD]. Autoimmune responses are involved in the pathophysiology of IBD, but their underlying pathways and target antigens have not yet been fully elucidated. Methods Autoantigenic targets in IBD were identified after separation of whole cell proteins isolated from neutrophils using two-dimensional electrophoresis and matrix assisted laser desorption ionization - time of flight mass spectrometry-based protein identification of the spots that displayed Western blotting signals with anti-neutrophil cytoplasmic antibody-positive sera. The prevalence of IgG, IgA and secretory IgA [sIgA] to chitinase 3-like protein 1 [CHI3L1] was analysed by enzyme-linked immunosorbent assays using recombinant CHI3L1 in 110 patients with Crohn's disease [CD], 95 with ulcerative colitis [UC], 126 with coeliac disease [CeD] and 86 healthy controls [HCs]. Results The 18-glycosylhydrolase family member CHI3L1 was identified as a neutrophil autoantigenic target. CD patients displayed significantly higher levels of IgG to CHI3L1 than patients with UC and CeD (p < 0.0001, respectively). IgA and sIgA to CHI3L1 was significantly higher in CD than in UC, CeD and HCs [p < 0.0001, respectively]. IgA and sIgA to CHI3L1 demonstrated the highest prevalence in CD [25.5\%, 28/110; and 41.8\%\%, 46/110] compared to HCs [2.3\%, 2/86; and 4.7\%\%, 4/86; p = 0.0015 and p < 0.0001] and are associated with a more complicated progression of CD. Conclusion CHI3L1 is a novel neutrophil autoantigenic target in CD. IgA and sIgA to CHI3L1 may serve as novel markers for CD and may facilitate the serological diagnosis of IBD.}, language = {en} } @misc{SowaMurugaiyanConradetal., author = {Sowa, Mandy and Murugaiyan, Jayaseelan and Conrad, Karsten and Laass, Martin W. and Bogdanos, Dimitrios Petrou and Papp, Maria and R{\"o}diger, Stefan and Roggenbuck, Dirk and Schierack, Peter}, title = {A novel neutrophil autoantigenic target in inflammatory bowel disease}, language = {en} } @misc{JurischkaDinterEfimovaetal., author = {Jurischka, Christoph and Dinter, Franziska and Efimova, Anastasia and Weiss, Romano and Schiebel, Juliane and Schulz, Christian and Fayziev, Bekzodjon and Schierack, Peter and Fischer, Thomas and R{\"o}diger, Stefan}, title = {An explorative study of polymers for 3D printing of bioanalytical test systems}, series = {Clinical Hemorheology and Microcirculation}, volume = {75}, journal = {Clinical Hemorheology and Microcirculation}, number = {1}, issn = {1875-8622}, doi = {10.3233/CH-190713}, pages = {57 -- 84}, abstract = {Background: The 3D printing is relevant as a manufacturing technology of functional models for forensic, pharmaceutical and bioanalytical applications such as drug delivery systems, sample preparation and point-of-care tests. Objective: Melting behavior and autofluorescence of materials are decisive for optimal printing and applicability of the product which are influenced by varying unknown additives. Methods: We have produced devices for bioanalytical applications from commercially available thermoplastic polymers using a melt-layer process. We characterized them by differential scanning calorimetry, fluorescence spectroscopy and functional assays (DNA capture assay, model for cell adhesion, bacterial adhesion and biofilm formation test). Results: From 14 tested colored, transparent and black materials we found only deep black acrylonitrile-butadiene-styrene (ABS) and some black polylactic acid (PLA) useable for fluorescence-based assays, with low autofluorescence only in the short-wave range of 300-400 nm. PLA was suitable for standard bioanalytical purposes due to a glass transition temperature of approximately 60°C, resistance to common laboratory chemicals and easy print processing. For temperature-critical methods, such as hybridization reactions up to 90°C, ABS was better suited. Conclusions: Autofluorescence was not a disadvantage per se but can also be used as a reference signal in assays. The rapid development of individual protocols for sample processing and analysis required the availability of a material with consistent quality over time. For fluorescence-based assays, the use of commercial standard materials did not seem to meet this requirement.}, language = {en} } @misc{WhaleSpiegelaereTrypsteenetal., author = {Whale, Alexandra S. and Spiegelaere, Ward De and Trypsteen, W. and Nour, Afif Abdel and Bae, Young-Kyung and Benes, Vladimir and Cleveland, Megan and Devonshire, Alison S. and Dong, Lianhua and Drandi, Daniela and Foy, Carole A. and Garson, Jeremy A. and He, Hua-Jun and Hellemans, Jan and Kubista, Mikael and Lievens, Antoon and Makrigiogos, Mike G. and M{\"u}ller, Reinhold D. and Nolan, Tania and O'Sullivan, Denise M. and Pfaffl, Michael W. and R{\"o}diger, Stefan and Romsos, Erica L. and Shipley, Gregory L. and Taly, Valerie and Untergasser, Andreas and Wittwer, Carl T. and Bustin, Stephen A. and Vandesompele, Jo and Huggett, Jim F.}, title = {The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020}, series = {Clinical Chemistry}, volume = {66}, journal = {Clinical Chemistry}, number = {8}, issn = {0009-9147}, doi = {10.1093/clinchem/hvaa125}, pages = {1012 -- 1029}, language = {en} } @misc{SchmidtSchierackGerberetal., author = {Schmidt, Carsten and Schierack, Peter and Gerber, Ulrike and Schr{\"o}der, Christian and Choi, Youngeun and Bald, Ilko and Lehmann, Werner and R{\"o}diger, Stefan}, title = {Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures}, series = {Langmuir}, volume = {36}, journal = {Langmuir}, number = {2}, issn = {1520-5827}, doi = {10.1021/acs.langmuir.9b02339}, pages = {628 -- 636}, language = {en} } @misc{BurdukiewiczSidorczukRafaczetal., author = {Burdukiewicz, Michał and Sidorczuk, Katarzyna and Rafacz, Dominik and Pietluch, Filip and Chilimoniuk, Jarosław and R{\"o}diger, Stefan and Przemysław, Gagat}, title = {Proteomic Screening for Prediction and Design of Antimicrobial Peptides with AmpGram}, series = {International Journal of Molecular Sciences}, volume = {21}, journal = {International Journal of Molecular Sciences}, number = {12}, issn = {1422-0067}, doi = {10.3390/ijms21124310}, pages = {13}, language = {en} } @misc{ReimannZengJakopecetal., author = {Reimann, Ronny and Zeng, Bo and Jakopec, Martin and Burdukiewicz, Michał and Petrick, Ingolf and Schierack, Peter and R{\"o}diger, Stefan}, title = {Classification of dead and living microalgae Chlorella vulgaris by bioimage informatics an machine learning}, series = {Algal Research}, volume = {48}, journal = {Algal Research}, issn = {2211-9264}, doi = {10.1016/j.algal.2020.101908}, pages = {11}, language = {en} } @misc{DeutschmannRoggenbuckSchieracketal., author = {Deutschmann, Claudia and Roggenbuck, Dirk and Schierack, Peter and R{\"o}diger, Stefan}, title = {Autoantibody testing by enzyme-linked immunosorbent assay-a case in which the solid phase decides on success and failure}, series = {Heliyon}, volume = {6}, journal = {Heliyon}, number = {1}, issn = {2405-8440}, doi = {10.1016/j.heliyon.2020.e03270}, pages = {6}, language = {en} } @misc{SchiebelNoackRoedigeretal., author = {Schiebel, Juliane and Noack, Jonas and R{\"o}diger, Stefan and Kammel, Anne and Menzel, Friederike and Schwibbert, Karin and Weise, Matthias and Weiss, Romano and B{\"o}hm, Alexander and Nitschke, J{\"o}rg and Elimport, Alexey and Roggenbuck, Dirk and Schierack, Peter}, title = {Analysis of three-dimensional biofilms on different material surfaces}, series = {Biomaterials Science}, volume = {8}, journal = {Biomaterials Science}, number = {12}, issn = {2047-4849}, doi = {10.1039/D0BM00455C}, pages = {3500 -- 3510}, language = {en} } @misc{DinterJurischkaWeissetal., author = {Dinter, Franziska and Jurischka, Christoph and Weiss, Romano and R{\"o}diger, Stefan}, title = {Multiparametrische Antik{\"o}rperdetektion f{\"u}r die Diagnostik}, series = {BIOspektrum}, volume = {26}, journal = {BIOspektrum}, number = {3}, issn = {1868-6249}, doi = {10.1077/s12268-020-1375-5}, pages = {265 -- 267}, language = {de} } @misc{LiedtkeSchroederRoggenbucketal., author = {Liedtke, Victoria and Schr{\"o}der, Christian and Roggenbuck, Dirk and Weiss, Romano and Stohwasser, Ralf and Schierack, Peter and R{\"o}diger, Stefan and Schenk, Lysann}, title = {LEDGF/p75 is required for an efficient DNA damage response}, series = {International Journal of Molecular Sciences}, volume = {22}, journal = {International Journal of Molecular Sciences}, number = {11}, doi = {10.3390/ijms22115866}, pages = {1 -- 16}, language = {en} } @misc{SchmidtBerghausBlessingetal., author = {Schmidt, Jonas and Berghaus, Sandro and Blessing, Frithjof and Wenzel, Folker and Herbeck, Holger and Blessing, Josef and Schierack, Peter and R{\"o}diger, Stefan and Roggenbuck, Dirk}, title = {Serological and viral genetic features of patients with COVID-19 in a selected German patient cohort-correlation with disease characteristics}, series = {GeroScience}, volume = {43}, journal = {GeroScience}, number = {5}, issn = {2509-2723}, doi = {10.1007/s11357-021-00443-w}, pages = {2249 -- 2264}, language = {en} } @misc{AdefioyeWeinreichRoedigeretal., author = {Adefioye, Olusolabomi J. and Weinreich, J{\"o}rg and R{\"o}diger, Stefan and Schierack, Peter and Olowe, Olugbenga Adekunle}, title = {Phylogenetic Characterization and Multilocus Sequence Typing of Extended-Spectrum Beta Lactamase-Producing Escherichia coli from Food-Producing Animals, Beef, and Humans in Southwest Nigeria}, series = {Microbial Drug Resistance}, volume = {27}, journal = {Microbial Drug Resistance}, number = {1}, issn = {1931-8448}, doi = {10.1089/mdr.2019.0397}, pages = {111 -- 120}, language = {en} } @misc{ChilimoniukGosiewskaSłowiketal., author = {Chilimoniuk, Jarosław and Gosiewska, Alicja and Słowik, Jadwiga and Weiss, Romano and Deckert, P. Markus and R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {coutfitteR: efficient selection of count distributions to assess DNA damage}, series = {Annals of Translational Medicine}, volume = {9}, journal = {Annals of Translational Medicine}, number = {7}, issn = {2305-5847}, doi = {10.21037/atm-20-6363}, language = {en} } @misc{HanschmannRoedigerKrameretal., author = {Hanschmann, Henning and R{\"o}diger, Stefan and Kramer, Toni and Hanschmann, Katrin and Steidle, Michael and Fingerle, Volker and Schmidt, Carsten and Lehmann, Werner and Schierack, Peter}, title = {LoopTag FRET Probe System for Multiplex qPCR Detection of Borrelia Species}, series = {Life}, volume = {11}, journal = {Life}, number = {11}, issn = {2075-1729}, doi = {10.3390/life11111163}, language = {en} } @misc{SchmidtBorcherdingThieleetal., author = {Schmidt, Carsten and Borcherding, Heike and Thiele, Thomas and Schedler, Uwe and Werner, Franziska and R{\"o}diger, Stefan and Roggenbuck, Dirk and Schierack, Peter}, title = {Fluorescence-encoded poly (methyl metharcylate) nanoparticles for a lateral flow assay detecting IgM autoantibodies in rheumatoid arthritis}, series = {Analytical biochemistry}, volume = {Vol. 633}, journal = {Analytical biochemistry}, issn = {1096-0309}, doi = {10.1016/journal.ppat.1010118}, language = {en} } @misc{KhanKolendaSchieracketal., author = {Khan, Muhammad Moman and Kolenda, Rafał and Schierack, Peter and Weinreich, J{\"o}rg and R{\"o}diger, Stefan and Schierack, Jakob and Stubbe, Michael and Lkhagvasuren, Davaa and Guenther, Sebastian and Schaufler, Katharina}, title = {Investigation of Commensal Escherichia coli Populations of Cormorant Hatchlings in the Absence of Anthropogenic Impacts in Remote Areas of West Mongolia}, series = {Microorganisms}, volume = {9}, journal = {Microorganisms}, number = {2}, issn = {2076-2607}, doi = {10.3390/microorganisms9020372}, language = {en} } @misc{SchmidtBerghausBlessingetal., author = {Schmidt, Jonas and Berghaus, Sandro and Blessing, Frithjof and Wenzel, Folker and Herbeck, Holger and Blessing, Josef and Schierack, Peter and R{\"o}diger, Stefan and Roggenbuck, Dirk}, title = {A semi-automated, isolation-free, high-throughput SARS-CoV-2 reverse transcriptase (RT) loop-mediated isothermal amplification (LAMP) test}, series = {Scientific reports}, volume = {11}, journal = {Scientific reports}, number = {1}, issn = {2045-2322}, doi = {10.1038/s41598-021-00827-0}, language = {en} } @misc{BartlitzKolendaChilimoniuketal., author = {Bartlitz, Christin and Kolenda, Rafał and Chilimoniuk, Jarosław and Grzymajlo, Krzysztof and R{\"o}diger, Stefan and Bauerfeind, Rolf and Ali, Aamir and Tchesnokovag, Veronika and Roggenbuck, Dirk and Schierack, Peter}, title = {Adhesion of Enteropathogenic, Enterotoxigenic, and Commensal Escherichia coli to the Major Zymogen Granule Membrane Glyoprotein 2}, series = {Applied abd Environmental Microbiology}, volume = {88}, journal = {Applied abd Environmental Microbiology}, number = {5}, issn = {1098-5536}, doi = {10.1128/aem.02279-21}, language = {en} } @misc{SchmidtKammelTanneretal., author = {Schmidt, Carsten and Kammel, Anne and Tanner, Julian A. and Kinghorn, Andrew B. and Khan, Muhammad Moman and Lehmann, Werner and Menger, Marcus and Schedler, Uwe and Schierack, Peter and R{\"o}diger, Stefan}, title = {A Multiparametic Fluorescence Assay for Screening Aptamer-Protein Interactions Based on Microbeads}, series = {Scientific Reports}, volume = {12}, journal = {Scientific Reports}, issn = {2045-2322}, doi = {10.1038/s41598-022-06817-0}, pages = {10}, language = {en} } @misc{FischerMarchettiDeschmannAssisetal., author = {Fischer, Thomas and Marchetti-Deschmann, Martina and Assis, Ana Cristina and Elad, Michal Levin and Algarra, Manuel and Barac, Marko and Bogdanovic Radovic, Iva and Cicconi, Flavio and Claes, Britt and Frascione, Nunzianda and George, Sony and Guedes, Alexandra and Heaton, Cameron and Heeren, Ron and Lasic, Violeta and Lerma, Jos{\´e} Luis and Valle Martinez de Yuso Garcia, Maria del and Nosko, Martin and O'Hara, John and Oshina, Ilze and Palucci, Antonio and Pawlaczyk, Aleksandra and Posp{\´i}škov{\´a}, Krist{\´y}na and de Puit, Marcel and Radodic, Ksenija and Rēpele, Māra and Ristova, Mimoza and Romolo, Francesco Saverio and Šafař{\´i}k, Ivo and Siketic, Zdravko and Spigulis, Janis and Szynkowska-Jozwik, Malgorzata Iwona and Tsiatsiuyeu, Andrei and Vella, Joanna and Dawson, Lorna and R{\"o}diger, Stefan and Francese, Simona}, title = {Profiling and imaging of forensic evidence - A pan-European forensic round robin study part 1: Document forgery}, series = {Science \& Justice}, volume = {62}, journal = {Science \& Justice}, number = {4}, issn = {1876-4452}, doi = {10.1016/j.scijus.2022.06.001}, pages = {433 -- 447}, language = {en} } @misc{LopensWunschMilkiewiczetal., author = {Lopens, Steffi and Wunsch, Ewa and Milkiewicz, Malgorzata and R{\"o}ber, Nadja and Zarske, Grit and Nasser, Abdullah and Conrad, Karsten and Laass, Martin W. and R{\"o}diger, Stefan and Krawczyk, Marcin and Roggenbuck, Dirk and Milkiewicz, Piotr}, title = {PR3-ANCAs Detected by Third-Generation ELISA Predicts Severe Disease and Poor Survival in Primary Sclerosing Cholangitis}, series = {Diagnostics}, volume = {12}, journal = {Diagnostics}, number = {11}, issn = {2075-4418}, doi = {10.3390/diagnostics12112682}, abstract = {A highly sensitive detection of anti-neutrophil cytoplasmic antibodies to serine proteinase-3 (PR3-ANCAs) aids in the serological diagnosis of autoimmune liver disorders and the prediction of severity in primary sclerosing cholangitis (PSC). Here, we evaluate a novel third-generation ELISA for the detection of PR3-ANCAs. In total, 309 patients with PSC, 51 with primary biliary cholangitis (PBC), and 120 healthy blood donors (BD) were analyzed. For the survival analysis in PSC, the outcome was defined as liver-transplantation-free survival during the follow-up. Positive PR3-ANCA levels were found in 74/309 (24.0\%) of patients with PSC. No BDs and one patient with PBC demonstrated PR3-ANCA positivity. PR3-ANCAs were revealed as independent predictors for a poor PSC outcome (study endpoint: liver transplantation/death, log-rank test, p = 0.02). PR3-ANCA positivity, lower albumin levels, and higher bilirubin concentrations were independent risks of a poor survival (Cox proportional-hazards regression analysis, p < 0.05). The Mayo risk score for PSC was associated with PR3-ANCA positivity (p = 0.01) and the disease severity assessed with a model of end-stage liver disease (MELD) and extended MELD-Na (p < 0.05). PR3-ANCAs detected by a third-generation ELISA are diagnostic and prognostic markers for PSC. Their wider use could help to identify patients who are at-risk of a more severe disease.}, language = {en} } @misc{AzamRoesslingGeitheetal., author = {Azam, Hafiz Muhammad Husnain and R{\"o}ßling, Rosa Ilse and Geithe, Christiane and Khan, Muhammad Moman and Dinter, Franziska and Hanack, Katja and Pr{\"u}ß, Harald and Husse, Britta and Roggenbuck, Dirk and Schierack, Peter and R{\"o}diger, Stefan}, title = {MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review}, series = {Frontiers in Molecular Neuroscience}, volume = {17}, journal = {Frontiers in Molecular Neuroscience}, publisher = {Frontiers Media S.A.}, issn = {1662-5099}, doi = {10.3389/fnmol.2024.1386735}, pages = {35}, abstract = {Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells—all indicative of disease progression—before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.}, language = {en} } @misc{ChilimoniukErolRoedigeretal., author = {Chilimoniuk, Jarosław and Erol, Anna and R{\"o}diger, Stefan and Burdukiewicz, Michał}, title = {Challenges and opportunities in processing NanoString nCounter data}, series = {Computational and Structural Biotechnology Journal}, volume = {23}, journal = {Computational and Structural Biotechnology Journal}, publisher = {Elsevier BV}, issn = {2001-0370}, doi = {10.1016/j.csbj.2024.04.061}, pages = {1951 -- 1958}, language = {en} } @misc{LopensSchierackKrauseetal., author = {Lopens, Steffi and Schierack, Peter and Krause, Jenny and Piaszczyński, Michał and Kr{\´o}l, Robert and Staroń, Robert and Krupa, Łukasz and Gutkowski, Krzysztof and Kruk, Beata and Grąt, Michał and Krawczyk, Marek and Patkowski, Waldemar and Glaser, Fabian and R{\"o}diger, Stefan and Grossmann, Kai and Pająk, Jacek and Milkiewicz, Piotr and Lammert, Frank and Zieniewicz, Krzysztof and Schramm, Christoph and Roggenbuck, Dirk and Krawczyk, Marcin}, title = {Antimicrobial glycoprotein 2 (GP2) in gallstones, bile fluid and peribiliary glands of patients with primary sclerosing cholangitis}, series = {Clinica Chimica Acta}, volume = {562}, journal = {Clinica Chimica Acta}, publisher = {Elsevier BV}, issn = {0009-8981}, doi = {10.1016/j.cca.2024.119841}, pages = {1 -- 8}, language = {en} } @misc{GeitheZengSchmidtetal., author = {Geithe, Christiane and Zeng, Bo and Schmidt, Carsten and Dinter, Franziska and Roggenbuck, Dirk and Lehmann, Werner and Dame, Gregory and Schierack, Peter and Hanack, Katja and R{\"o}diger, Stefan}, title = {A multiplex microchamber diffusion assay for the antibody-based detection of microRNAs on randomly ordered microbeads}, series = {Biosensors and Bioelectronics: X}, volume = {18 (2024)}, journal = {Biosensors and Bioelectronics: X}, publisher = {Elsevier BV}, issn = {2590-1370}, doi = {10.1016/j.biosx.2024.100484}, pages = {1 -- 7}, language = {en} } @misc{RoedigerKoeglerBirkholz, author = {R{\"o}diger, Stefan and K{\"o}gler, Martin and Birkholz, Mario}, title = {Open-Source software, fediverse and custom ROMs as tools for a sustainable internet}, series = {2024 Electronics Goes Green 2024+ (EGG)}, journal = {2024 Electronics Goes Green 2024+ (EGG)}, publisher = {IEEE}, address = {Berlin}, doi = {10.23919/EGG62010.2024.10631179}, pages = {1 -- 13}, language = {en} } @misc{BrauckhoffRoediger, author = {Brauckhoff, Tim and R{\"o}diger, Stefan}, title = {BiopixR - extended vignette for bioimage analysis package in R}, doi = {10.5281/zenodo.12744223}, language = {en} } @misc{LiedtkeWeissSkifovetal., author = {Liedtke, Victoria and Weiss, Romano and Skifov, Anastasia and R{\"o}diger, Stefan and Schenk, Lysann}, title = {Fully automated viability and toxicity screening - areliable all-in-one attempt}, series = {Cancer Medicine}, volume = {13}, journal = {Cancer Medicine}, number = {12}, publisher = {Wiley}, issn = {2045-7634}, doi = {10.1002/cam4.7392}, pages = {16}, abstract = {The CRISPR/Cas9 technology is nowadays a common tool for genome editing to achieve new insights into, for example, diagnostics and therapeutics in cancer and genetic disorders. Cell proliferation and anticancer drug response studies are widely used to evaluate the impact of editing. However, these assays are often time-consuming, expensive, and reproducibility is an issue. To overcome this, we developed a fast and cheap assay that combines a fully automated multispectral fluorescence microscopy platform with a nuclei staining and open-source software analysis.Here, we generated different LEDGF/p75 model cell lines to validate the effect on proliferation and chemosensitivity. Therefore, a fast protocol for an optimized all-in-one attempt for cytotoxicity screenings and proliferation analysis of adherent cells in a 96-well plate format was established using differential staining with two fluorescent dyes (Hoechst 33342 and propidium iodide) for live/dead cell discrimination. Subsequently, an automated cell nuclei count and analysis were performed using bioimage informatics.With the new established assay technology, up to 50,000 cells/well can be detected and analyzed in a 96-well plate, resulting in a fast and accurate verification of viability and proliferation with consistency of 98\% compared to manual counting. Our screening revealed that LEDGF depletion using CRISPR/Cas9 showed a diminished proliferation and chemosensitivity independent of cell line origin. Moreover, LEDGF depletion caused a significant increase in 𝛾H2AX foci, indicating a substantial increase in DNA double strand breaks. LEDGF/p75 overexpression enhanced proliferation and chemoresistance underlining the role of LEDGF in DNA damage response.Independent of cancer cell type, LEDGF/p75 is a central player in DNA damage repair and is implicated in chemoresistance. Moreover, our automated fluorescence biosensor technology allowed fast and reliable data acquisition without any fixation or additional washing steps. Additionally, data analysis was implemented using the modular open-source software that can be adapted as needed.}, language = {en} } @misc{BrauckhoffKiefferRoediger, author = {Brauckhoff, Tim and Kieffer, Coline and R{\"o}diger, Stefan}, title = {Extracting Insights from biological images}, series = {Journal of Open Source Software}, volume = {9}, journal = {Journal of Open Source Software}, number = {102}, issn = {2475-9066}, doi = {10.21105/joss.07074}, pages = {7}, language = {en} } @misc{LiedtkeRoseHiemannetal., author = {Liedtke, Victoria and Rose, Laura and Hiemann, Rico and Nasser, Abdullah and R{\"o}diger, Stefan and Bonaventura, Alena and Winkler, Laura and Sowa, Mandy and St{\"o}ckle, Michael and Schierack, Peter and Junker, Kerstin and Roggenbuck, Dirk}, title = {Over-Expression of LEDGF/p75 in HEp-2 Cells Enhances Autoimmune IgG Response in Patients with Benign Prostatic Hyperplasia—A Novel Diagnostic Approach with Therapeutic Consequence?}, series = {International Journal of Molecular Sciences}, volume = {24}, journal = {International Journal of Molecular Sciences}, number = {7}, issn = {1422-0067}, doi = {10.3390/ijms24076166}, abstract = {Lens epithelium-derived growth factor splice variant of 75 kDa (LEDGF/p75) is an autoantigen over-expressed in solid tumors and acts as a stress-related transcriptional co-activator. Participation of autoimmune responses in the pathophysiology of benign prostatic hyperplasia (PBH) and a corresponding immunosuppressive therapy by TNFalpha antagonists has been recently suggested. Thus, autoAb testing could aid in the diagnosis of BPH patients profiting from such therapy. We generated CRISPR/Cas9 modified HEp-2 LEDGF knock-out (KO) and HEp-2 LEDGF/p75 over-expressing (OE) cells and examined IgG autoantibody reactivity to LEDGF/p75 in patients with prostate cancer (PCa, n = 89), bladder cancer (BCa, n = 116), benign prostatic hyperplasia (BPH, n = 103), and blood donors (BD, n = 60) by indirect immunofluorescence assay (IFA). Surprisingly, we could not detect elevated binding of autoAbs against LEDGF/p75 in cancer patients, but autoAb reactivity to LEDGF/p75 OE cells in about 50\% of patients with BPH was unexpectedly significantly increased. Furthermore, a line immunoassay enabling the detection of 18 different autoAbs revealed a significantly increased occurrence of anti-dsDNA autoAbs in 34\% of BPH patients in contrast to tumor patients and BD. This finding was confirmed by anti-mitochondrial (mDNA) autoAb detection with the Crithidia luciliae immunofluorescence test, which also showed a significantly higher prevalence (34\%) of anti-mDNA autoAbs in BPH. In summary, our study provided further evidence for the occurrence of autoimmune responses in BPH. Furthermore, LEDGF/p75 over-expression renders HEp-2 cells more autoantigenic and an ideal target for autoAb analysis in BPH with a potential therapy consequence.}, language = {en} } @misc{RoeiBorisYehudaetal., author = {Roei, Tulchinsky and Boris, Gilburd and Yehuda, Shovman and Milena, Tocut and Eleanor, Zeruya and Ariel, Binyaminov and Tima, Davidson and B{\"u}ttner, Thomas and Nasser, Abdullah and Michel, Juliane and R{\"o}diger, Stefan and Schierack, Peter and Howard, Amital and Roggenbuck, Dirk and Yehuda, Shoenfeld and Ora, Shovman}, title = {CytoBead ANA 2 assay : a novel method for the detection of antinuclear antibodies}, series = {Scientific reports}, volume = {15}, journal = {Scientific reports}, number = {1}, publisher = {Nature Publishing Group UK}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-025-04583-3}, pages = {1 -- 11}, abstract = {Detection of anti-nuclear autoantibodies (ANA) is based on a two-step algorithm including indirect immunofluorescence (IIF) on HEp2 cells and subsequent reflex/confirmatory testing for specific autoantibodies. Simultaneous cell- and microbead-based autoantibody detection by IIF may be utilized for the evaluation of systemic autoimmune rheumatic diseases (SARDs). In the present study, we assessed the performance of CytoBead ANA 2 in the detection of ANA and ANA-specific autoantibodies, compared to ANA IIF and BioPlex™ 2200. We also tested the ability of CytoBead ANA DFS-70 to identify dense-fine speckled (DFS) pattern associated with anti-DFS70 antibodies in non-SARDs patients. Hundred-twelve routine sera samples were assessed by manual CytoBead ANA 2 for the presence of ANA and specific autoantibodies. In parallel, these samples were analyzed by HEp2 ANA IIF test and a subsequent multiplexed assay BioPlex™ 2200 ANA. Twenty-nine ANA-positive samples obtained from non-SARDs patients and exhibiting DFS pattern by ANA IIF were further tested by CytoBead ANA DFS-70. A substantial agreement was observed between classical ANA IIF and manual CytoBead ANA 2 for the detection of ANA (k = 0.74). Discordant results were mainly associated with the presence of anti-SSA/Ro antibodies detected by CytoBead ANA 2 in ANA IIF negative patients. A good to almost perfect agreement was found between CytoBead ANA 2 and BioPlex™ 2200 for detection of specific antibodies with kappa values ranging from 0.70 to 0.90. Twenty samples (68.9\%) obtained from 29 ANA IIF positive without SARDs patients exhibited DFS pattern in CytoBead ANA DFS-70, which confirmed the presence of anti-DFS70 antibodies. The diagnostic performance of manual CytoBead ANA 2 for ANA screening and detection of ANA specific antibodies is comparable to the diagnostic performance of ANA IIF followed by BioPlex™ 2200. This novel one-step assay enables simultaneous ANA screening and confirmation and represents a promising alternative approach to the time-consuming and costly two-tier ANA analysis.}, language = {en} } @misc{AzamMumtazRoedigeretal., author = {Azam, Hafiz Muhammad Husnain and Mumtaz, Mehvish and R{\"o}diger, Stefan and Schierack, Peter and Hussain, Nazim and Aisha, Ambreen}, title = {MicroRNAs in neurodegenerative diseases : from molecular mechanisms to clinical biomarkers, detection methods and therapeutic strategies—advances and challenges}, series = {Neurological sciences}, journal = {Neurological sciences}, publisher = {Springer}, address = {Milano}, issn = {1590-3478}, doi = {10.1007/s10072-025-08419-w}, pages = {43}, abstract = {Neurodegenerative diseases (NDDs) pose significant challenges in early detection and treatment due to their complex pathophysiology and heterogeneous clinical presentations. MicroRNAs (miRNAs), small noncoding RNAs that regulate gene expression, have emerged as promising diagnostic biomarkers and therapeutic targets in NDDs. Pathological examination of affected tissues reveals early synaptic dysfunction, protein misfolding, and neuroinflammation occur prior to overt clinical symptoms, highlighting the importance of sensitive diagnostics approaches in prodromal stages. This review summarizes for researchers on the role of miRNAs in NDDs by examining their diagnostic potential in biofluids such as blood and cerebrospinal fluid, and their therapeutic applicability through inhibition or replacement strategies. Literature from peer-reviewed databases was assessed with a focus on recent advances in molecular detection platforms, computational modeling of miRNA-mRNA interactions, and preclinical/clinical investigations. More than 2600 human miRNAs have been identified, collectively regulating over half of mammalian protein-coding genes. Quantitative methodologies, particularly reverse transcription quantitative PCR (RT-qPCR), enable reliable miRNA profiling, facilitating early diagnosis and prognosis of NDDs. Therapeutic strategies, including antagomirs, mimics, sponges and viral or non-viral delivery systems, show promise in modulating disease pathways. However, significant challenges remain, including variability in miRNA extraction and quantification protocols, off-target effects, delivery barriers across the blood brain barrier and limited reproducibility across studies. MiRNAs represent a class of molecular tools with potential to transform diagnostics and therapeutics in NDDs. Future research should prioritize methodological standardization, validation in large multicenter cohorts, and improved computational approaches to elucidate miRNA-mediated regulatory networks in NDDs. Replication studies and translational research are essential harnessing the the full clinical utility of miRNAs in the management of Alzheimer disease, Parkinson disease and other NDDs.}, language = {en} }