@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{NazAhmadSarwaretal., author = {Naz, Fizza and Ahmad, Abrar and Sarwar, Yasra and Khan, Muhammad Moman and Schierack, Peter and Rauf, Waqar and Ali, Aamir}, title = {Characterization of Salmonella enterica Biofilms and Antibiofilm Effect of Carvacrol and 2-Aminobenzimidazole}, series = {Foodborne Pathogens and Disease}, volume = {21}, journal = {Foodborne Pathogens and Disease}, number = {1}, publisher = {Mary Ann Liebert Inc.}, issn = {1535-3141}, doi = {10.1089/fpd.2023.0044}, pages = {52 -- 60}, language = {en} } @misc{KhanMushtaqAbbasetal., author = {Khan, Muhammad Moman and Mushtaq, Muhammad Ahmed and Abbas, Nayyar and Fatima, Fariha and Gibbon, Marjorie J. and Schierack, Peter and Mohsin, Mashkoor}, title = {Occurrence, antimicrobial resistance and genomic features of Klebsiella pneumoniae from broiler chicken in Faisalabad, Pakistan}, series = {Frontiers in Veterinary Science}, volume = {11}, journal = {Frontiers in Veterinary Science}, publisher = {Frontiers Media S.A.}, issn = {2297-1769}, doi = {10.3389/fvets.2024.1433124}, pages = {7}, abstract = {IntroductionThe dissemination of antimicrobial resistance (AMR) in critical priority pathogens is a significant threat. Non-clinical reservoirs of AMR, such as agriculture and food production facilities, may contribute to the transmission of clinically relevant pathogens such as multidrug-resistant (MDR) Klebsiella pneumoniae. There is currently very limited knowledge regarding the population structure and genomic diversity of K. pneumoniae in poultry production in Pakistan.MethodsWe explored healthy broilers in a commercial farm from Faisalabad, Pakistan, and identified six K. pneumoniae strains from 100 broiler birds. We characterized the strains, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing.ResultsThe evaluation of antimicrobial susceptibility revealed that all the strains were MDR. Genomic analysis showed that 3/6 strains belonged to ST152, harbouring acquired resistance aminoglycosides [aadA2, aph(4′)-Ia], β-lactams (blaSHV-187, blaLAP2), fosfomycin (fosA6), tetracycline (tetA), trimethoprim (dfrA12), quinolone (qnrS1), sulphonamides (sul2) and phenicol (floR). All the strains harboured the efflux pump genes oqxA, oqxB, emrR, kpnG, kpnH, kpnF, baeR, mtdB and mtdC. All six strains encoded identical virulence profiles possessing six genes, i.e., ureA, iutA, entB, allS, fimH and mrkD. Phylogenomic analysis of the dominant sequence type (ST152) present in our dataset with publicly available genomes showed that the isolates clustered to strains mainly from human sources and could pose a potential threat to food safety and public health.DiscussionThe combination of these findings with antimicrobial use data would allow a better understanding of the selective pressures that may be driving the spread of AMR. This is the first report of MDR K. pneumoniae isolated from broiler hens in Pakistan, and the finding suggests that routine surveillance of WHO critical priority pathogens in such settings would be beneficial to the development of effective control strategies to reduce AMR.}, 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{KhanAliKolendaetal., author = {Khan, Muhammad Moman and Ali, Aamir and Kolenda, Rafał and Olowe, Olugbenga Adekunle and Weinreich, J{\"o}rg and Li, Ganwu and Schierack, Peter}, title = {The role of AJB35136 and fdtA genes in biofilm formation by avian pathogenic Escherichia coli}, series = {BMC Veterinary Research}, volume = {19}, journal = {BMC Veterinary Research}, issn = {1746-6148}, doi = {10.1186/s12917-023-03672-7}, language = {en} } @book{OPUS4-35290, title = {Applications of biopolymers in science, biotechnology, and engineering}, editor = {Reghunadhan, Arunima and H, Akhina and Thomas, Sabu}, edition = {1}, publisher = {Wiley}, isbn = {9781119783442}, doi = {10.1002/9781119783473}, pages = {432}, language = {en} } @incollection{MumtazHussainSalametal., author = {Mumtaz, Mehvish and Hussain, Nazim and Salam, Sidra and Azam, Hafiz Muhammad Husnain and Łukasik, Natalia and Kim, Tak H. and Santos, Jos{\´e} Cleiton Sousa dos and Schmidt, Jens Ejbye}, title = {Chitosan-based nanomaterials for removal of water pollutants}, series = {Chitosan-Based Hybrid Nanomaterials}, booktitle = {Chitosan-Based Hybrid Nanomaterials}, publisher = {Elsevier}, isbn = {9780443218910}, doi = {10.1016/B978-0-443-21891-0.00016-0}, pages = {291 -- 318}, 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} }