1. Data from publication: Functional genomics screening in Chlamydomonas reinhardtii maps the genetic landscape of tolerance to paraquat and diuronTim Godec, Carissa Bleker, Katja Stare, Tjaša Lukan, Valentina Levak, Magda Tušek-Žnidarič, Alexander Betz, Tina Kosjek, Katarina Petra Van Midden, Marina Klemenčič, Francesco Trenti, Graziano Guella, Kristina Sepčić, Friedrich Fauser, Weronika Patena, Martin C. Jonikas, Maruša Kerenčič, Tina Eleršek, Mélanie Pietri, Thomas Rodet, Urban Bren, Marko Jukič, Samo Lešnik, Anže Županič, 2026, complete scientific database of research data Keywords: functional genomics, Chlamydomonas reinhardtii, paraquat, diuron, ecotoxicology
Published in DiRROS: 22.07.2026; Views: 222; Downloads: 140
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2. Functional genomics screening in Chlamydomonas reinhardtii maps the genetic landscape of tolerance to paraquat and diuronTim Godec, Carissa Bleker, Katja Stare, Tjaša Lukan, Valentina Levak, Magda Tušek-Žnidarič, Tina Kosjek, Katarina Petra Van Midden, Marina Klemenčič, Kristina Sepčić, Maruša Kerenčič, Tina Eleršek, Urban Bren, Marko Jukič, Samo Lešnik, Anže Županič, 2026, original scientific article Abstract: Functional genomics offers a powerful, unbiased approach to elucidating the molecular mechanisms underlying the toxicity of environmental pollutants. In this study, we applied genome-wide screening in Chlamydomonas reinhardtii to investigate two classical herbicides: paraquat and diuron. Our screen successfully uncovered critical nuclear-encoded pathways that govern susceptibility. For both herbicides, we identified genes regulating the assembly and maintenance of the photosynthetic machinery, highlighting the central role of nuclear control over these chloroplast-localized targets. Beyond these target-related factors, we discovered novel nontarget-site resistance mechanisms. For paraquat, we identified intracellular trafficking as the central determinant of toxicity, experimentally characterizing a P5B ATPase transporter and a fatty acid elongation pathway whose disruption, we propose, converges on the same endomembrane delivery route through sphingolipid depletion. In contrast, our screening data suggest that diuron tolerance may be associated with a metabolic strategy focused on energy conservation, where the inactivation of specific NADPH-consuming enzymes could preserve reducing power for essential antioxidant defense. Collectively, these findings demonstrate that functional genomics can reveal novel, complex modes of action even for well-characterized chemicals, providing the mechanistic resolution required to advance modern ecotoxicological risk assessments.
Keywords: paraquat, diuron
Published in DiRROS: 09.06.2026; Views: 256; Downloads: 236
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3. PBPK model code associated to the journal article entitled: "Making PBPK models more reproducible in practice" : Version v2Elena Domínguez-Romero, Stanislav Mazurenko, Martin Scheringer, Vitor A. P. Martins dos Santos, Chris T Evelo, Mihail Anton, John M. Hancock, Anže Županič, Maria Suarez-Diez, 2024, complete scientific database of research data Abstract: Physiologically-based pharmacokinetic (PBPK) model code associated to the journal article by: E. Domínguez-Romero, S. Mazurenko, M. Scheringer, V. A. P. Martins dos Santos, C. T. Evelo, M. Anton, J. M. Hancock, A. Županič, M. Suarez-Diez, entitled: Making PBPK models more reproducible in practice (Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae569, https://doi.org/10.1093/bib/bbae569).
The code is provided in MATLAB and SBML formats. The following files can be found here:
"PBPK_code_EDR_et_al_vs4.m": model code in MATLAB format. This is the 4th version of the code. The mathematical model is described by Domínguez-Romero et al., and more succinctly explained within the code (annotations). When this code is run in MATLAB, we obtain the next file:
"Model_variables_numeric_results.xls": numeric results obtained by model simulation in MATLAB.
"SM2_PBPK_code_EDR_et_al_final4_test_trigger.xml": model code in SBML format, obtained by conversion of the MATLAB code, by using "Model ODE Converter for Creating Automated SBML Interoperability (MOCCASIN)” (Gómez et al., 2016) and COPASI tools (Tiwari et al., 2021). More details about the conversion can be found in Domínguez-Romero et al. (2024).
Keywords: pharmacokinetics, pharmacodynamics, mathematical modelling, standards, model code, reproducibility, SBML, MATLAB, systems biology
Published in DiRROS: 08.05.2026; Views: 312; Downloads: 424
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4. Odprta znanost : Mala Loža, Koper, od 29. julija do 18. avgusta 2025 in Gallusovo nabrežje, Ljubljana, od 28. avgusta do 6. oktobra 20252025, exhibition Keywords: odprta znanost, občanska znanost, raziskovalni podatki, podatkovni svetovalec, repozitoriji, projekt SPOZNAJ
Published in DiRROS: 06.11.2025; Views: 1037; Downloads: 1037
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5. Predstavitev Priročnika o načrtovanju ravnanja z raziskovalnimi podatkiSonja Bezjak, Maja Zagorščak, Irena Vipavc Brvar, Anže Županič, 2025, other monographs and other completed works Abstract: Predstavitev je predstavila zasnovo in vsebino novega spletnega Priročnika o načrtovanju ravnanja z raziskovalnimi podatki (2025) ter pokazala njegovo praktično uporabo na konkretnih primerih iz naravoslovja in družboslovja.
Keywords: načrt ravnanja z raziskovalnimi podatki, odprti podatki, podatkovna objava, načela FAIR, odprta znanost
Published in DiRROS: 28.10.2025; Views: 877; Downloads: 515
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6. Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response : version v3Tjaša Lukan, Kristina Gruden, Anže Županič, Tjaša Mahkovec Povalej, 2021, complete scientific database of research data Abstract: We performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant Ny‐1-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. This dataset s a deposit of all the raw microscopy images of the study, plus the relevant metadata in ISA-tab compliant folder structure. After receiving reviews, we have made an additional experiment using a ROS inhibitor. The raw and processed data for this is in a separate file: _S_chlROS_inhibitor.zip
Keywords: cell signalling, chloroplasts, microscopy, ISA-tab, potato virus Y, redox responses, cell death, spatiotemporal analysis
Published in DiRROS: 24.10.2025; Views: 857; Downloads: 576
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7. Systems biology to unravel Western diet-associated triggers in inflammatory bowel diseaseŠpela Konjar, Evgen Benedik, Marko Šestan, Marc Veldhoen, Anže Županič, 2025, review article Keywords: IBD, western diet, immune cels, microbiota, systems biology
Published in DiRROS: 24.10.2025; Views: 892; Downloads: 391
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8. Predstavitev programskih orodij Python in RMaja Zagorščak, Carissa Bleker, Jan Zrimec, Marko Petek, Anže Županič, 2024, other educational material Keywords: podatki, ravnanje s podatki, ravnanje z raziskovalnimi podatki, raziskovalni podatki, odprta znanost, programska orodja, Python, R
Published in DiRROS: 26.05.2025; Views: 1196; Downloads: 1060
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9. Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potatoMaja Zagorščak, Lamis Abdelhakim, Natalia Yaneth Rodriguez-Granados, Carissa Bleker, Andrej Blejec, Jan Zrimec, Špela Baebler, Anže Županič, Maruša Pompe Novak, Kristina Gruden, 2025, original scientific article Abstract: Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.
Keywords: potato, Solanum tuberosum, abiotic stress responses, heat, drought, waterlogging, multi-omics, integrative omics, adaptomics, panomics
Published in DiRROS: 14.04.2025; Views: 1433; Downloads: 1159
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10. Orodja za delo z delotokiMarko Vidak, Bojan Kverh, Polonca Ferk, Branimir Leskošek, Maja Zagorščak, Nadja Franziska Nolte, Carissa Bleker, Marko Petek, Anže Županič, 2024, other monographs and other completed works Keywords: odprti podatki, odprta znanost, delo z delotoki, projekt Spoznaj, okolje Galaxy, raziskovalni podatki, uporabljanje podatkov
Published in DiRROS: 12.03.2025; Views: 1345; Downloads: 672
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