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Item type: Item , Restoring semi-natural grasslands in Central Europe with plant material transfer – achievements, success factors, and knowledge transfer(2025) Sommer, LeonhardSince the industrial revolution, land use changes and intensification of use have drastically reduced the area of species-rich, semi-natural grasslands in Central Europe. Active restoration of these ecosystems is therefore necessary and increasingly demanded by legislation. One method to (re-)introduce target plant species is the transfer of seed-containing plant material cut from species-rich, semi-natural donor sites. Given the urgency of the restoration task, the aim of this thesis is to contribute to understanding the success factors of this method, particularly in practice. In a first study, 20 recipient sites of floodplain meadow restoration in Hesse, Germany, were revisited and investigated for vegetation composition in comparison to their corresponding donor sites 13-16 years after plant material transfer. To assess the potential for livestock feeding, biomass yield and energy contents were measured, too. In a second study, 41 recipient-donor site pairs from practical grassland restoration projects in different regions of Germany and Luxembourg spanning a broad moisture gradient were investigated. Vegetation was recorded, and soil analyses and information on restoration from the practice partners were used for success factor identification. In a third study, 33 practitioners of grassland restoration with plant material transfer were interviewed to compare their views on the topic to European scientific literature. All three studies underline the critical importance of abiotic site conditions supporting the target plant communities. A frequent long-term problem is too high productivity of recipient sites, particularly in floodplain meadows. Site conditions, along with competition for the introduced plant species, are strongly dependent on the previous state of recipient sites. Raw soils, e.g., obtained by topsoil removal, provide low-competitive, nutrient-poor conditions, often enhancing restoration success. Generally, competition for the introduced species is lowered by adequate soil preparation, whose effect may, however, diminish over time. Harvest time for the plant material is decisive for the pool of transferable target species, and supplementing this pool by additional introduction methods, such as sowing, is useful. For maintenance of restored grassland communities, appropriate low-intensive post-restoration management is necessary. Sufficient biomass yield and energy content enable integration in feeding rations for livestock, buffering the costs of management. Practitioner interviews revealed that overarching factors such as project organisation, trust-building, and experience strongly influence how well the previously mentioned conditions can be met. To support grassland restoration in the coming decades, a challenge increased by climate change, intense knowledge exchange between science and practice and among practitioners is advised.Item type: Item , Einfluss einer pulmonalen Ballonangioplastie bei Patienten mit chronisch thromboembolischer pulmonaler Hypertonie auf elektrokardiographische Parameter(2025) Ley, Lukas MaximilianEinleitung: Die chronisch thromboembolische pulmonale Hypertonie (CTEPH) ist der wichtigste Vertreter der Gruppe 4 der pulmonalen Hypertonie und tritt bei etwa 2-3% der Überlebenden einer Lungenembolie als Langzeitfolge auf. Eine der verfügbaren Therapiemöglichkeiten ist die pulmonale Ballonangioplastie (BPA). Die CTEPH kann mit typischen elektrokardiographischen Zeichen einhergehen, welche sich nach BPA bessern können. Material und Methoden: Die vorliegende Studie schloss von März 2014 bis Oktober 2020 retrospektiv 150 Patienten (53% Frauen, 47% Männer, medianes Alter: 64 Jahre) ein. Alle Patienten erhielten ein 12-Kanal-EKG und eine Rechtsherzkatheteruntersuchung vor, sowie sechs Monate nach BPA. Hauptziel der Studie war es, die Prävalenz elektrokardiographischer Pathologien bei der CTEPH und deren Veränderung nach BPA darzustellen. Ergebnisse: Die vorliegende Studie konnte bestätigen, dass typische elektrokardiographische Pathologien der CTEPH beobachtet werden, diese sich nach hämodynamisch erfolgreicher BPA zurückbilden und mit hämodynamischen Parametern korrelieren können. Besonders auffällig war der Hauptparameter "R V1, V2 + S I, aVL - S V1". Er korrelierte mit dem mittleren pulmonalarteriellen Druck (mPAP) und pulmonalvaskulären Widerstand (PVR, r-Werte: 0,372-0,519, p < 0,001). Zudem verbesserte sich dieser statistisch signifikant nach BPA (47% vs. 29%, p < 0,001). Bei Analyse der Subgruppen war zu beobachten, dass bei einer hämodynamisch schwereren CTEPH häufiger und deutlichere elektrokardiographische Pathologien zu detektieren waren und ein EKG bei Patienten mit milder CTEPH auch vollkommen unauffällig sein konnte. Schlussfolgerungen: Die Ergebnisse der vorliegenden Studie stimmen mit der aktuellen Studienlage überein. Trotz zahlreicher Vorteile kann das EKG aktuell nur Hinweise auf eine CTEPH liefern, da es diesem, vor allem in Anfangsstadien, an Sensitivität mangelt und es allein weder die CTEPH sicher diagnostizieren noch ausschließen kann. Weitere potenzielle Einsatzgebiete wie die Vorhersage der kardiopulmonalen Hämodynamik, die Kontrolle der Therapieeffektivität, die Unterstützung beim Treffen von Therapieentscheidungen, die Risikostratifizierung oder die CTEPH-Früherkennung sowie der Hauptparameter „R V1, V2 + S I, aVL - S V1” sollten in weiteren Studien genauer erforscht werden.Item type: Item , Development of a pipeline for spatial transcriptome analysis of samples from Hodgkin's lymphoma patients(2025-12-17) Melanie KeckOVERVIEW Automated pipeline for spatial transcriptomics analysis of classical Hodgkin lymphoma samples using 10x Genomics Visium low-density platform. Includes preprocessing (Space Ranger), quality control, batch correction (Harmony, scVI), and downstream analysis. Master's thesis, Justus Liebig University Giessen (2026). CONTENTS - Bash script for automated Space Ranger preprocessing - JupyterLab notebooks for quality control, batch correction, and downstream analysis - PDF reports documenting all analysis steps and results - HTML tables with QC metrics, correlation matrices, and differential expression results - Figures and visualizations from all analyses - Test dataset for pipeline validation (mouse spleen, GEO: GSE254652) TECHNICAL REQUIREMENTS - Ubuntu 24.04.2 LTS, Space Ranger v3.1.3, Python 3.12.10 - Python packages: Scanpy (v1.10.4), Squidpy (v1.6.5), harmonypy (v0.0.10), scVI (v1.3.1.post1) - Hardware: Minimum 40 GB RAM, 4 CPU cores recommended - Reference files: refdata-gex-GRCh38-2020-A, Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A USAGE 1. Prepare input files (SampleSheet.csv, Aggregation.csv) 2. Configure paths in script.sh and collect_output.py 3. Run preprocessing: bash script.sh 4. Generate metadata: python collect_output.py 5. Update base paths in JupyterLab notebooks 6. Execute JupyterLab notebooks sequentially For detailed documentation, see README.pdfItem type: Item , Deciphering Self-Assembly Mechanisms and Chemical Reactions of Organic Building Blocks on Metal Surfaces by Chemical Bond Imaging(2025-09-24) Wiche, MiguelIn recent years, the novel field of on-surface synthesis has been established as one of the main tools for constructing customized, low-dimensional organic nanostructures via bottom-up approaches on atomically flat metal substrates. The self-assembly of the molecular precursors, a process that often serves as pre-step of the on-surface reaction, determines the precise local arrangement of atoms and bonds in neighboring molecules, thus playing a decisive role in product formation. Thereby, intermolecular interactions between hydrogen and fluorine atoms have proven to be a valuable tool to steer molecular alignments. In this work, the mainly unexplored intermolecular hydrogen-fluorine interaction is systematically investigated on inert Au(111) and reactive Cu(111) substrates, using a linear, unilaterally fluorinated 1,2,10,11,12,14-hexafluoropentacene molecule as a model system. In the combined scanning tunneling microscopy and chemical bond imaging study, the local arrangement of hydrogen and fluorine atoms in neighboring molecules is determined in the picometer range and angular variations of a few degrees. While on Au(111) the intermolecular interactions between the molecules are the main contributor to the self-assembly, the higher reactivity of Cu(111) results in different adsorption geometries and molecular arrangements. The highly precise self-assembly study provides new insights into the on-surface interaction of hydrogen and fluorine atoms, thereby highlighting its significance for the field of on-surface synthesis. An on-surface reaction that solely takes place using halogenated precursors is the on-surface Ullmann coupling reaction, which enables the formation of covalent carbon-carbon bonds with the underlying metal surface as a catalyst. However, when applying Ullmann coupling reaction steps, complex self-assembly mechanisms can occur when halogenated precursors interact with the metal surface. Further, cleaved halogens adsorbed on the surface may potentially inhibit the reaction steps. Hence, there is a growing demand for halogen-free precursors for on-surface reactions. Recently, it has been demonstrated that halogen-free (6)Cycloparaphenylene ((6)CPP) molecules are suited to thermally induce a ring-opening polymerization reaction for the synthesis of graphene and biphenylene nanoribbons of confined widths. However, the mechanism of the ring-opening polymerization and the use of cycloparaphenylenes as precursors have not been investigated sufficiently. To contribute to the fundamental understanding of this remarkable reaction, in this thesis we systematically investigate the influence of the ring strain, which decreases with increasing ring size, using a set of cycloparaphenylenes of different sizes ((6)CPP vs. (8)CPP vs. (10)CPP). Our results demonstrate that the ring-opening polymerization is facilitated when using smaller, highly strained cycloparaphenylenes. For larger molecules with lower strain energies, the initial ring-opening is hampered, leading to only partial polymerization for (8)CPP and no polymerization in case of (10)CPP. Additionally, dehydrogenation of individual phenyl rings in intact molecules is observed for (8)CPP and (10)CPP, which further impedes the polymerization reaction.Item type: Item , The Effects of DNA Repair Pathway Engineering on CRISPR-Mediated Genome Editing in Neuronal Cells(2025) Alabudeeb, FatimahInherited retinal dystrophies are a group of genetically and clinically heterogeneous disorders that vary in their clinical presentation and progression, possibly leading to blindness. So far, about 332 genes, most expressed in photoreceptors, have been identified to be associated with these diseases. The relatively new genome editing field, particularly CRISPR-Cas9 mediated genome editing technology, which introduces DNA double-strand breaks (DSBs) that are subsequently repaired by the cells' repair systems, has recently drawn much attention. The major repair pathways are non-homologous end-joining (NHEJ) and homology-directed repair (HDR). One of the main obstacles to its application in the retina is the limited knowledge of DNA repair in photoreceptors. This work aims to analyze the DNA repair mechanisms, improve CRISPR Cas9 genome editing efficacy by modulating and engineering the DNA repair pathways in mature neurons using the human inducible Neurogenin iPS (iNGN) cell line, and validate it as an in vitro model system. These cells are human-induced pluripotent stem cells that differentiate into mature neurons within 4 days. In addition, the iNGN TET3KO cell line was also investigated to determine the impact of the TET3 protein at various differentiation stages. To achieve this, the iNGN cell lines and a control cell line, HEK293T cells, were transfected with BRET reporter assay plasmid using Cas9 and the inducible Cas systems (iCas). Promoter optimizations were done by replacing the CMV promoter, which can be silenced and suppressed in certain cell types, with a sustained EF1α promoter. Applying the Cas9 system, iNGN WT and iNGN TET3KO cells were tested throughout the differentiation process. Moreover, the modifications of PARP1 protein levels using PARP1 overexpression or knockout plasmids were necessary to study its influence on the DNA repair pathways of different cell lines. The BRET reporter assay was the primary quantitative technique used. The results showed decreased frameshift rates for the undifferentiated iNGN using the iCas system compared to the Cas9 system, and along with failure to use its timing control advantage, the Cas9 system was mainly used for the remaining experiments. The undifferentiated iNGN TET3KO cells' frameshift rates, as well as at the beginning of differentiation, were significantly higher than iNGN WT ones. Furthermore, the frameshift rate results of the TET3KO overexpressed cells resembled those of iNGN WT cells. After PARP1 modulation, the frameshift rates of PARP1 downregulation were greater throughout the differentiation process of the iNGNs, regardless of the HDR template addition. Interestingly, the results of the iNGN TET3KO cells were higher than those of the WT cells. For future assessment, the generation and application of iNGNs TLR3 cell lines is essential to verify the results obtained using the BRET reporter assay at the genomic level.