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: 235; Downloads: 143
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2. In silico characterisation of a novel SARS-CoV-2 envelope protein inhibitor and in vitro validation against murine coronavirusNina Kobe, Lennart Dreisewerd, Miha Lukšič, Matic Pavlin, Uroš Grošelj, Črtomir Podlipnik, Mojca Janc, Živa Lengar, Polona Mrak, Magda Tušek-Žnidarič, Maruša Pompe Novak, Urška Kuhar, Peter Hostnik, Federica Dattola, Tea Carletti, Alessandro Marcello, Polona Kogovšek, 2026, original scientific article Abstract: The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses a challenge to current therapies and emphasises the need for targets that are less susceptible to mutation. The SARS-CoV-2 envelope protein (Epro) is a highly conserved viroporin and is of central importance to the viral life cycle, yet it remains underexplored as a therapeutic target. In this study, we have identified and characterised a novel lead candidate (LC) − (S)-N-(2-((1S,3S,5S,7S)-adamantan-2-yl)ethyl)-2-(butylamino)-3-(1H-indol-3-yl)propanamide − for inhibition of the SARS-CoV-2 Epro ion channel using combined in silico and in vitro approaches. Molecular dynamics (MD) simulations showed that LC forms stable complexes at the N-terminal vestibule, with key interactions at GLU8, THR9, THR11, ASN15, and LEU18, and a calculated binding affinity higher than that of the reference compound rimantadine within the applied MD/molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) framework. Results of in vitro experiments indicated that LC inhibits the model coronavirus murine hepatitis virus at late stages of the viral cycle. Activity under co-treatment conditions further suggests a direct virucidal effect or interference with early entry stages; an EC50 of approximately 12 μM was within the same micromolar range as those observed for the reference Epro inhibitors 5-(N,N-hexamethylene)amiloride and rimantadine. Quantitative PCR experiments showed delayed RNA replication in LC-treated infected cells, while light and transmission electron microscopy displayed the reduced release of virions and prevention of cell lysis. These results emphasise the central role of the Epro ion channel in the coronavirus life cycle and present LC as a promising candidate for the further development of novel coronavirus inhibitors.
Keywords: SARS-CoV-2 envelope protein, viroporin, ion channel blockers, molecular docking, molecular dynamics simulations, drug discovery, murine hepatitis virus, in vitro
Published in DiRROS: 11.06.2026; Views: 240; Downloads: 252
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3. 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: 258; Downloads: 240
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4. Data from manuscript: In silico characterisation of a novel SARS-CoV-2 envelope protein inhibitor and in vitro validation against murine coronavirus : Version v1Nina Kobe, Lennart Dreisewerd, Miha Lukšič, Matic Pavlin, Uroš Grošelj, Črtomir Podlipnik, Mojca Janc, Živa Lengar, Polona Mrak, Magda Tušek-Žnidarič, Maruša Pompe Novak, Urška Kuhar, Peter Hostnik, Federica Dattola, Tea Carletti, Alessandro Marcello, Polona Kogovšek, 2025, complete scientific database of research data Keywords: SARS-CoV-2 envelope protein, viroporin, ion channel blockers, molecular docking, molecular dynamics simulations, drug discovery, murine hepatitis virus, in vitro
Published in DiRROS: 22.05.2026; Views: 287; Downloads: 364
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5. HIV protein Nef expression in human microglia drives the release of distinct Nef-containing extracellular vesiclesTeja Lavrin, Jure Loboda, Jana Ferdin, Valentina Levak, Simona Sitar, Marija Holcar, Nataša Resnik, Matjaž Stenovec, Alenka Trampuš-Bakija, Peter Veranič, Ema Žagar, Magda Tušek-Žnidarič, Pia Pužar Dominkuš, Metka Lenassi, 2025, original scientific article Abstract: Aim: Human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) persist in effectively treated HIV-infected individuals, in part due to HIV reservoirs in brain microglia, which express low levels of viral proteins such as Nef. This study aimed to elucidate how microglia release Nef into the extracellular space, where it exerts its biological functions. Methods: Here, we systematically characterized extracellular particles released from immortalized human microglia (h-microglia) expressing Nef alone or after HIV infection. Importantly, we established a novel h-microglia model harboring a stably integrated Nef tagged with green fluorescent protein (Nef.GFP) transgene under an inducible promoter. Extracellular vesicles (EVs) were enriched from culture media and analyzed for morphology, size, concentration and molecular composition, including Nef content, by (super-resolution) fluorescence microscopy, (immunogold) transmission electron microscopy, asymmetric flow field-flow fractionation coupled to a multi-angle light-scattering detector, nanoparticle tracking analysis, and nano-flow cytometry and immunoblotting. Results: Nef.GFP expression increased particle release up to 11.7-fold compared with controls or known stimulants adenosine triphosphate (ATP) and ionomycin. Compared to the latter, the particles were also significantly smaller (root mean square radius, Rrms = 172 nm) and displayed unique protein and density profiles. All data support the EV nature of the released particles. Approximately half of the Nef.GFP-induced EVs contained Nef (45.5% ± 15.8%), with immunogold labeling confirming its intraluminal localization. Notably, infection with HIV isolates NL4-3 and YU-2 likewise produced Nef-positive EVs distinct from virions. Conclusion: Our findings importantly contribute to understanding the source and characteristics of extracellular Nef in the central nervous system of HIV infected individuals and offer new tools to study HIV Nef biology. Nef-laden EVs should be further investigated as potential therapeutic targets in HAND.
Keywords: human immunodeficiency virus (HIV), microglia, protein Nef, extracellular vesicles (EVs), HIV-associated neurocognitive disorder (HAND)
Published in DiRROS: 13.04.2026; Views: 320; Downloads: 218
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6. Metadata from: Functionality of potato virus Y coat protein in cell-to-cell movement dynamics is defined by its N-terminal regionAnže Vozelj, Tjaša Mahkovec Povalej, Katja Stare, Magda Tušek-Žnidarič, Katarina Bačnik, Valentina Levak, Ion Gutiérrez-Aguirre, Marjetka Podobnik, Kristina Gruden, Anna Coll Rius, Tjaša Lukan, 2025, complete scientific database of research data Keywords: potato virus Y, coat protein, viral movement, point mutations, Solanum tuberosum
Published in DiRROS: 31.03.2026; Views: 390; Downloads: 414
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7. Species-specific structural adaptation of the potyviral coat protein in virions and virus-like particlesNeža Koritnik, Andreja Kežar, Luka Kavčič, Magda Tušek-Žnidarič, Adrijana Leonardi, Swarnalok De, Maija Pollari, Kristiina Mäkinen, Marjetka Podobnik, 2026, original scientific article Published in DiRROS: 20.03.2026; Views: 455; Downloads: 314
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8. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus YLuka Kavčič, Andreja Kežar, Neža Koritnik, Magda Tušek-Žnidarič, Tajda Klobučar, Žiga Vičič, Franci Merzel, Ellie Holden, Justin L. P. Benesch, Marjetka Podobnik, 2024, original scientific article Published in DiRROS: 09.03.2026; Views: 458; Downloads: 349
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9. Functionality of potato virus Y coat protein in cell-to-cell movement dynamics is defined by its N-terminal regionAnže Vozelj, Tjaša Mahkovec Povalej, Katja Stare, Magda Tušek-Žnidarič, Katarina Bačnik, Valentina Levak, Ion Gutiérrez-Aguirre, Marjetka Podobnik, Kristina Gruden, Anna Coll Rius, Tjaša Lukan, 2025, original scientific article Abstract: Potato virus Y (PVY) is one of the top 10 economically most important plant viruses and responsible for major yield losses. We previously suggested the involvement of the N-terminal region of PVY coat protein (CP) in PVY spread. By constructing different N-terminal deletion mutants of the PVY N605 strain, we here show that deletions of 40 or more amino acid residues from the N-terminal region of the CP resulted in the PVY multiplication limited to primary infected cells in Nicotiana clevelandii plants. Deletion of 26 residues profoundly impaired PVY cell-to-cell movement and prevented systemic PVY spread, while deletions of 19-23 residues allowed delayed systemic PVY spread. Introduced point mutations in the identified region prevent (S21G) or delay (G20P) PVY movement. In summary, this work shows the significance of the CP N-terminus for movement of the PVY.
Keywords: potato virus Y, potato, coat proteins, viral movement, point mutations
Published in DiRROS: 18.12.2025; Views: 1181; Downloads: 581
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10. Clinical and structural features of sperm head vacuoles in men included in the in vitro fertilization programmeNina Fekonja, Jasna Štrus, Magda Tušek-Žnidarič, Katja Knez, Eda Vrtačnik-Bokal, Ivan Verdenik, Irma Virant-Klun, 2014, original scientific article Abstract: The human sperm head vacuoles and their role in male infertility are still poorly understood. The aim of this study was to identify the clinical and ultrastructural features of human sperm head vacuoles in men included in the in vitro fertilization programme: men with normal (normozoospermia) and impaired sperm morphology (teratozoospermia). The sperm samples were observed under 6000-time magnification using motile sperm organelle morphology examination (MSOME). The proportion of sperm with head vacuoles was evaluated and related to the outcome of in vitro fertilization. The sperm of men with impaired sperm morphology was characterized by a higher proportion of sperm head vacuoles. The sperm head vacuoles were related to impaired semen quality (sperm concentration, motility, and morphology) but were not influenced by male factors (semen volume, height, age, weight, or body mass index). Moreover, sperm head vacuoles were related to impaired fertilization rate merely after classical in vitro fertilization (IVF), while there was no relation to pregnancy. In a subgroup of men, the sperm was fixed and observed by transmission electron microscopy (TEM). The ultrastructural study revealed that sperm head vacuoles are large nuclear indentations of various sizes and positions, packed with membranous material organized in membrane whorls (MW).
Keywords: human sperm head vacuoles, male infertility
Published in DiRROS: 04.03.2025; Views: 979; Downloads: 1173
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