Biology subjects

Bekeschus, S.

Publications and source records attributed to Bekeschus, S..

4 recordsLinked to original sources

bioRxiv2026

Bioimaging Data Management Workflow for Plasma Medicine

Bioimaging experiments in plasma medicine generate complex datasets that go beyond conventional imaging studies by combining microscopy data with heterogeneous metadata from biological experiments and highly parameterized gas plasma treatments. Plasma exposure conditions, such as device configuration, gas composition, and treatment conditions, are critical determinants of biological outcome, yet they are rarely captured in a standardized, machine-readable, and reusable manner. To address this gap, we present a research data management (RDM) workflow that operationalizes the Findable, Accessible, Interoperable, and Reusable (FAIR) principles across the bioimaging data lifecycle in plasma medicine. The workflow is implemented as a structured pipeline integrating open-source tools, including OMERO for image data management, eLabFTW as an electronic laboratory notebook, Adamant for schema-driven metadata collection, and Micro-Meta App for standardized documentation of microscopy acquisition settings that are connected via programming interfaces to enable persistent linkage of metadata to image datasets using standardized annotations. The workflow is documented in a reproducible tutorial with an open-source Python Jupyter notebook hosted on GitHub. By integrating plasma treatment metadata with imaging data, this approach improves reproducibility, cross-study comparability, and data reuse in plasma medicine research.

bioinformatics↗

bioRxiv2024

High-throughput differentiation of human blood vessel organoids reveals overlapping and distinct functions of the cerebral cavernous malformation proteins

Cerebral cavernous malformations (CCMs) are clusters of thin-walled enlarged blood vessels in the central nervous system that are prone to recurrent hemorrhage and can occur in both sporadic and familial forms. The familial form results from loss-of-function variants in the CCM1, CCM2, or CCM3 gene. Despite a better understanding of CCM pathogenesis in recent years, it is still unclear why CCM3 mutations often lead to a more aggressive phenotype than CCM1 or CCM2 variants. By combining high-throughput differentiation of blood vessel organoids from human induced pluripotent stem cells (hiPSCs) with a CCM1, CCM2, or CCM3 knockout, single-cell RNA sequencing, and high-content imaging, we uncovered both shared and distinct functions of the CCM proteins. While there was a significant overlap of differentially expressed genes in fibroblasts across all three knockout conditions, inactivation of CCM1, CCM2, or CCM3 also led to specific gene expression patterns in neuronal, mesenchymal, and endothelial cell populations, respectively. Taking advantage of the different fluorescent labels of the hiPSCs, we could also visualize the abnormal expansion of CCM1 and CCM3 knockout cells when differentiated together with wild-type cells into mosaic blood vessel organoids. In contrast, CCM2 knockout cells showed even reduced proliferation. These observations may help to explain the less severe clinical course in individuals with a pathogenic variant in CCM2 and to decode the molecular and cellular heterogeneity in CCM disease. Finally, the ability to differentiate blood vessel organoids in a 96-well format will further facilitate their use in drug discovery and other biomedical research studies. STATEMENTS AND DECLARATIONSO_ST_ABSConflicts of interest statementC_ST_ABSThe authors declare no competing interests. The here described protocol for high-throughput organoid synthesis has been filed as a patent application at the European Patent Office (Process number: EP24213596.0) Author contribution statementMR, DSk, and UF designed the study. DSk, VS, LM, and RAP performed most of the functional experiments. SH and TA performed the CAM assays. SR performed the immunohistochemical stainings. SB, DSi, DSk, and VS performed the confocal microscopy and high-content imaging analyses. AE, CB, and EMB performed the scRNA sequencing analysis. AW and CAH performed and analyzed the karyotyping of the hiPSC clones. DSk, RAP, VS, KC, MR, and SB analyzed the data. DSk, VS, LM, and MR prepared figures. All authors contributed to the interpretation of the results. DSk, RAP, VS, and MR drafted the manuscript, and all authors contributed to writing. Ethics statementThis study does not involve human participants or animal subjects. Availability of data and materialsAll relevant data are published within the paper and the supplementary files. ScRNA sequencing data can be accessed through the Gene Expression Omnibus (GEO) database (record number: GSE276497).

molecular biology↗

bioRxiv2024

The use of 3D-printers as plotters opens up a new world in performing 2D migration analyses

Scratch wound healing assays remain one of the most commonly used 2D migration assays to obtain a broad overview of the migration behavior of cultured cells. They are easy to perform and cost-effective but not standardized in terms of the geometric dimensions of the scratch, e.g., the scratch width and straightness of the line, especially when performed manually. Furthermore, conventional scratch assays only include a single scratch. This leads to the evaluation of a restricted cell population within the culture plates but not of all cells grown in the chamber. There are commercially available scratch-makers that are highly expensive and lack advanced functions such as scratching complex patterns. However, such complex scratch formations would make it possible to assess the entire cell population in a chamber and evaluate the scratchs impact on, for example, migration-associated protein expression. To address this, we developed a novel method utilizing 3D printers as 2D plotters to allow repeatable scratch dimensions for varying pipette tips. This open-source and cost-effective system can be performed with any plate format from any manufacturer under culture hood conditions. The 2D plotter-based method we developed and validated provides highly reproducible and consistent scratch parameters for in vitro migration analyses.

bioengineering↗

bioRxiv2018

Effects on cell viability, growth and morphology of C. albicans SC5314 biofilms after kINPen(R)09 plasma treatment

Microorganisms are predominantly organized in biofilms, where cells live in dense communities and are more resistant to external stresses compared to their planktonic counterparts. With in vitro experiments, the susceptibility of Candida albicans biofilms to a non-thermal plasma treatment (plasma source kINP(R)09), in terms of growth, survival, and cell viability was investigated. Behind that background, the C. albicans strain SC5314 (ATCC(R) MYA-2876) was plasma treated for different time periods (30 s, 60 s, 120 s, 180 s, 300 s). The results of experiments embracing colony forming units, fluorescence LIVE/DEAD assays, and XTT assays revealed a negative influence of the plasma treatment on the proliferation ability, vitality, and the metabolism of C. albicans biofilms, respectively. Morphological analysis of plasma-treated biofilms using atomic force microscopy supported the indications for lethal plasma effects concomitant with membrane disruptions and the loss of intracellular fluid. Controversial to other publications, fluorescence- and confocal laser scanning-microscopic inspection of plasma-treated biofilms indicated, that an inactivation of cells mainly appeared on the bottom side of the biofilms. If this inactivation leads to a detachment of the biofilms from the overgrown surface, it might offer completely new approaches in the plasma treatment of biofilms. Because of its biochemical-mechanical mode of action, resistances of microbial cells against plasma are unknown at this state of research.

microbiology↗