Goethe University Data Repository (GUDe)
The archiving and publication platform for scientific research data at Goethe University Frankfurt.
The Goethe University Data Repository (GUDe) provides a platform for its members to electronically archive, share, and publish their research data. GUDe is jointly operated by the University Library and the University Data Center of the Goethe University. The metadata of all public content is freely available and indexed by search engines as well as scientific web services. GUDe follows the FAIR principles for long-term accessibility (minimum 10 years), allows for reliable citation via DOIs as well as cooperative access to non-public data and operates on DSpace-CRIS v7.
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- Research DataNucleotide-resolved conformational analysis of nascent RNA chains within the bacterial transcription elongation complex by MAS-DNP solid-state NMR2026-08-28In all kingdoms of life, multi-subunit RNA polymerases transcribe DNA to RNA. Both genomic DNA and newly transcribed RNA play key roles in transcription initiation, elongation, and termination. For example, a stretch of uridine residues at the 3′-end of the nascent RNA chain serves as a trigger to terminate transcription, release the nascent RNA chain and disassemble bacterial transcription elongation complexes (EC). It has remained unclear how the transcript can trigger termination if poly-uridine stretches are synthesized. Here, we establish an approach that combines site-selective ¹³C/¹⁵N labeling of uridines with magic-angle-spinning dynamic nuclear polarization (MAS-DNP) NMR to probe the nascent transcript residue by residue within a reconstituted, stalled Escherichia coli transcript elongation complex. We read out the 3′-terminal U-tract in the free RNA and in complexes stalled at two registers (h+1, h+5) to investigate conformational heterogeneity in the rU-dA hybrid duplex. Our results suggest that the internal uridines adopt a stable A-form (C3′-endo) conformation in the hybrid duplex. This conformation remains unchanged within the EC, whereas the 3′ -terminal residue is selectively perturbed within the complex. Solid-state NMR data collected on tailored isotopically labelled ECs resolve single-residue differences in conformation inside an assembled transcription complex, opening a route to study the nascent RNA at sites relevant to pausing and termination by MAS-DNP.
2 2 - Research DataStructural landscape and dynamics of SARS-CoV-2 RNA genome circularization2026-08-27RNA viruses possess strictly conserved RNA segments that adopt local structures and act as regulatory cis-acting elements. In addition, long-range RNA-RNA interactions between distant parts of their genome provide additional layers of regulatory control. In SARS‑CoV‑2, crosslinking experiments identified multiple long-range interactions within the genome, including the longest distant interaction between nucleotides in the 5’- and the 3’‑terminal, untranslated regions (UTR’s). Formation of this interaction requires opening of the 5’SL3 element in the 5’-UTR, which contains the transcription regulatory core sequence (TRS‑L), and of the 3’SL3base element in the 3’-UTR. Here, we investigate the minimal sequence context required for formation of this long-range interaction. We determine the alternative secondary structures adopted by these elements, their thermodynamic stability, and the stability of individual base pairs. Furthermore, we quantify equilibrium populations and exchange kinetics between the circularization duplex and the alternative local structures. We investigate duplex formation with larger, native-like UTR constructs, determining populations similar to those of the minimal constructs. Finally, we demonstrate that circularization is substantially less favorable in subgenomic RNAs than in the genomic RNA, suggesting that genome circularization may contribute to discrimination between functions involving either genomic or subgenomic RNAs during the viral life cycle.
1 11 - Research DataSmall Molecule Modulation of TERRA RNA Quadruplex Reprograms ALT-Telomere Maintenance2026-08-21Telomeric repeat–containing RNA (TERRA) plays a central role in telomere maintenance in telomerase-negative cancers that employ the alternative lengthening of telomeres (ALT) pathway; however, its RNA G-quadruplex (rG4) structures remain underexplored as chemical targets. Here, we report a structure-guided approach to selectively modulate TERRA rG4 using an indoloquinoxaline-based small-molecule scaffold. Biophysical analyses confirm high-affinity and selective binding, while NMR and computational studies identify terminal tetrad stacking as the dominant binding mode of the ligand to the TERRA rG4. Ligand engagement disrupts the TERRA–TRF2 interaction (ELISA, EMSA) and alters TERRA abundance (qRT-PCR). Transcriptomic (RNA-seq) analysis reveals ligand-induced differential expression of ALT-associated genes and DNA metabolism pathways. In ALT-positive U2OS cells, the ligand localizes to the nucleus, induces telomere-associated DNA damage, and triggers S-phase arrest and apoptosis. These findings establish TERRA rG4 as a chemically addressable structural element in ALT biology and demonstrate the potential of small molecules to probe and modulate long non-coding RNA (lncRNA-)–mediated genome maintenance.
22 4 - Research DataTEI/XML encoded transcription Na_50-796 from the Arthur Schopenhauer Legacy2026-08-18This document is a TEI/XML encoded transcription of the document Na_50-796 from the Arthur Schopenhauer Legacy - 'Schopenhauer-Archive': "Rechtfertigung wegen erhobener Vorwürfe" from Juliane Dorothea Trosiener to Johanna Schopenhauer. Transcribed by Rüdiger Weyer, TEI encoded by Hannah Völker (https://sammlungen.ub.uni-frankfurt.de/schopenhauer/content/titleinfo/4235122)
11 1 - Research DataTEI/XML encoded transcription Na_50-887 from the Arthur Schopenhauer Legacy2026-08-13This document is a TEI/XML encoded transcription of the document Na_50-887 from the Arthur Schopenhauer Legacy - 'Schopenhauer-Archive': "Enttäuschung über die vorhandenen Schreibfertigkeiten des Sohnes" from Heinrich Floris Schopenhauer to Arthur Schopenhauer. Transcribed and TEI encoded by Hannah Völker (https://sammlungen.ub.uni-frankfurt.de/schopenhauer/content/titleinfo/4235042)
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- Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-w5e5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2022 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (to be submitted to Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
1658 1238 - Research DataThe global water resources and use model WaterGAP v2.2e - model output driven by gswp3-era5 and historical setup of direct human impacts2023-10-20Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download model output for the time period 1901-2019 that was computed by driving WaterGAP v2.2e by four alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. For two climate datasets, model runs up to 2021 or 2023 are available. For comparison, output of a version of WaterGAP v2.2d that is calibrated to the same dataset of observed streamflow as WaterGAP v2.2e is provided. Each of the climate forcing-model version combinations is run in two socio-economic settings, histsoc and nosoc. In nosoc, human water use is set to zero and man-made reservoirs are assumed to be non-existant. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. The most important and requested model outputs (total water storage variations, streamflow and water use) are evaluated against observation data. Standard model output is described as well as the specifics of the WaterGAP contribution within the ISIMIP framework. Müller Schmied, H., Cáceres, D., Eisner, S., Flörke, M., Herbert, C., Niemann, C., Peiris, T. A., Popat, E., Portmann, F. T., Reinecke, R., Schumacher, M., Shadkam, S., Telteu, C.-E., Trautmann, T., Döll, P. (2021): The global water resources and use model WaterGAP v2.2d: Model description and evaluation. Geosci. Model Dev., 14, 1037–1079. https://doi.org/10.5194/gmd-14-1037-2021
1071 1208 - Research DataThe global water resources and use model WaterGAP v2.2e - daily water storage model output driven by gswp3-era5 and historical setup of direct human impacts2024-04-04Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download daily model output for water storage variables for the time period 1901-2019 (2023) that was computed by driving WaterGAP v2.2e by two alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. Here, the single water storage compartments and terrestrial (total) water storage are provided.
540 456 - Research DataThe global water resources and use model WaterGAP v2.2e - daily water storage model output driven by gswp3-w5e5 and historical setup of direct human impacts2024-04-04Trautmann, TimAckermann, SebastianCáceres, DeniseFlörke, MartinaGerdener, HelenaKynast, EllenPeiris, Thedini AsaliSchiebener, LeonieSchumacher, MaikeAssessing global freshwater resources and human water use is of value for a number of needs but challenging. The global water use and water availability model WaterGAP has been in development since 1996 and has served a range of applications such as assessments of global water resources and water stress, also under the impact of climate change, drought hazard quantification, Life Cycle Assessments, water (over)use and consequently depletion of water resources and a better understanding of terrestrial water storage variations (jointly with satellite observations). Here, the reader can download daily model output for water storage variables for the time period 1901-2019 (2023) that was computed by driving WaterGAP v2.2e by two alternative climate datasets (climate forcings) that were generated in the ISIMIP context (https://www.isimip.org) and are described in https://data.isimip.org/10.48364/ISIMIP.982724. In the paper connected to this dataset (in review with Geoscientific Model Development), the newest model version, WaterGAP v2.2e is described by providing the modifications to the previous version v2.2d (Müller Schmied et al. 2021) and the corresponding changes in model output. Here, the single water storage compartments and terrestrial (total) water storage are provided.
489 248 - Research DataA j_eff 12 Kitaev material on the triangular lattice: The case of NaRuO22023-06-07Motivated by recent reports of a quantum disordered ground state in the triangular lattice compound NaRuO$_2$, we derive a $j_{\rm eff}=1/2$ magnetic model for this system by means of first-principles calculations. The pseudospin Hamiltonian is dominated by bond-dependent off-diagonal $\Gamma$ interactions, complemented by a ferromagnetic Heisenberg exchange and a notably \emph{antiferromagnetic} Kitaev term. In addition to bilinear interactions, we find a sizable four-spin ring exchange contribution with a \emph{strongly anisotropic} character, which has been so far overlooked when modeling Kitaev materials. The analysis of the magnetic model, based on the minimization of the classical energy and exact diagonalization of the quantum Hamiltonian, points toward the existence of a rather robust easy-plane ferromagnetic order, which cannot be easily destabilized by physically relevant perturbations.
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