@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} } @misc{KhanMushtaqSulemanetal., author = {Khan, Muhammad Moman and Mushtaq, Muhammad Ahmed and Suleman, Muhammad and Ahmed, Umer and Ashraf, Muhammad Faisal and Aslam, Rizwan and Mohsin, Mashkoor and R{\"o}diger, Stefan and Sarwar, Yasra and Schierack, Peter and Ali, Aamir}, title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan : a 16S rRNA gene-based metagenomics study}, series = {Poultry science}, volume = {104}, journal = {Poultry science}, number = {6}, publisher = {Elsevier BV}, address = {Amsterdam}, issn = {0032-5791}, doi = {10.1016/j.psj.2025.105089}, pages = {1 -- 11}, abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 \% of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.}, language = {en} } @misc{BrauckhoffRublackRoediger, author = {Brauckhoff, Tim and Rublack, Julius and R{\"o}diger, Stefan}, title = {Exploring image analysis in R :applications and advancements}, series = {The R journal}, volume = {17}, journal = {The R journal}, number = {3}, publisher = {The R Foundation}, address = {Frederiksberg}, issn = {2073-4859}, doi = {10.32614/rj-2025-030}, pages = {212 -- 260}, abstract = {This review offers an overview of image processing packages in R, covering applications such as multiplex imaging, cell tracking, and general-purpose tools. We found 38 R packages for image analysis, with adimpro and EBImage being the oldest, published in 2006, and biopixR among the newest, released in 2024. Of these packages, over 90 \% are still active, with two-thirds receiving updates within the last 1.5 years. The pivotal role of bioimage informatics in life sciences is emphasized in this review, along with the ongoing advancements of R's functionality through novel code releases. It focuses on complete analysis pipelines for extracting valuable information from biological images and includes real-world examples. Demonstrating how researchers can use R to tackle new scientific challenges in image analysis, the review provides a comprehensive understanding of R's utility in this field.}, language = {en} } @misc{BustinRuijtervandenHoffetal., author = {Bustin, Stephen A and Ruijter, Jan M and van den Hoff, Maurice J B and Kubista, Mikael and Pfaffl, Michael W and Shipley, Gregory L and Tran, Nham and R{\"o}diger, Stefan and Untergasser, Andreas and Mueller, Reinhold and Nolan, Tania and Milavec, Mojca and Burns, Malcolm J and Huggett, Jim F and Vandesompele, Jo and Wittwer, Carl T}, title = {MIQE 2.0 : revision of the minimum information for publication of quantitative real-time PCR experiments guidelines}, series = {Clinical chemistry}, volume = {71}, journal = {Clinical chemistry}, number = {6}, publisher = {Oxford University Press (OUP)}, address = {Washington, DC ; Oxford}, issn = {0009-9147}, doi = {10.1093/clinchem/hvaf043}, pages = {634 -- 651}, abstract = {Background In 2009, the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines established standards for the design, execution, and reporting of quantitative PCR (qPCR) in research. The expansion of qPCR into numerous new domains has driven the development of new reagents, methods, consumables, and instruments, requiring revisions to best practices that are tailored to the evolving complexities of contemporary qPCR applications. Content Transparent, clear, and comprehensive description and reporting of all experimental details are necessary to ensure the repeatability and reproducibility of qPCR results. These revised MIQE guidelines reflect recent advances in qPCR technology, offering clear recommendations for sample handling, assay design, and validation, along with guidance on qPCR data analysis. Instrument manufacturers are encouraged to enable the export of raw data to facilitate thorough analyses and re-evaluation by manuscript reviewers and interested researchers. The guidelines emphasize that quantification cycle (Cq) values should be converted into efficiency-corrected target quantities and reported with prediction intervals, along with detection limits and dynamic ranges for each target, based on the chosen quantification method. Additionally, best practices for normalization and quality control are outlined and reporting requirements have been clarified and streamlined. The aim is to encourage researchers to provide all necessary information without undue burden, thereby promoting more rigorous and reproducible qPCR research. Summary Building on the collaborative efforts of an international team of researchers, we present updates, simplifications, and new recommendations to the original MIQE guidelines, designed to maintain their relevance and applicability in the context of emerging technologies and evolving qPCR applications.}, language = {en} } @misc{WeissLiedtkeRoediger, author = {Weiss, Romano and Liedtke, Victoria and R{\"o}diger, Stefan}, title = {Cannabidiol does not cause DNA double-strand breaks in a human liver-derived cell model}, series = {Journal of cannabis research}, volume = {8}, journal = {Journal of cannabis research}, number = {1}, publisher = {Springer Science and Business Media LLC}, issn = {2522-5782}, doi = {10.1186/s42238-025-00365-w}, pages = {1 -- 15}, abstract = {Background Cannabidiol (CBD) is a non-psychoactive cannabinoid with potential therapeutic applications, including anti-inflammatory, analgesic, and anticancer effects. However, experts raised concerns about its potential to induce DNA damage and chromosomal aberrations at low concentrations. Notably, these studies used liver cell lines, which may not fully reflect the metabolic processing of CBD, potentially limiting the generalizability of their findings. This study investigated the short time effects of CBD on DNA double-strand breaks (DSBs) and proliferation in the human liver-derived cell line HepG2. Methods HepG2 cells were treated with CBD (5 - 50 , 3 - 72h incubation). To investigate potential imbalances in the expression of cannabinoid receptors 1 and 2 (CB1 / CB2) within HepG2 cells, we examined their expression using Western blot analysis. We hypothesized that such an imbalance could be associated with pathogenic processes. Double-strand breaks were then detected (5 Etoposide (ETP) served as positive control) via indirect immunofluorescence analysis using H2AX and 53BP1 antibodies, followed by quantification of DSB foci. Results Expression of CB2 but not CB1 was downregulated by 30 \% in HepG2 cells after exposure to 5 CBD (24h incubation; 0.05) and 70 \% downregulated after exposure to 50 CBD (24h incubation; 0.01). This effect was dose-dependent. Whilst ETP induced dose dependent DSBs, we could not confirm findings by others that CBD significantly increases the number of H2AX and 53BP1 foci between 5 and 50 (3h incubation; 0.05). Conclusion In our model, CBD stimulated the cells, as confirmed by modulation of CB2 expression as well as changes in intracellular cAMP. Our results show that CBD in ranges between 5 to 50 does not significantly increase the amount of DNA double strand breaks in HepG2 cells compared to the control. However, we did observe a significant reduction in cell proliferation and a significant increase in intracellular cAMP levels following CBD treatment.}, language = {en} }