691. On the potential of ensemble forecasting for the prediction of meteotsunamis in the Balearic Islands : sensitivity to atmospheric model parameterizationsBaptiste Mourre, A. Santana, A. Buils, L. Gautreau, Matjaž Ličer, Agusti Jansá, B. Casas, B. Amengual, Joaquín Tintoré, 2021, izvirni znanstveni članek Povzetek: This study investigates the potential of ensemble forecasting using full realistic high-resolution nested atmosphere–ocean models for the prediction of meteotsunamis in Ciutadella (Menorca, Spain). The sensitivity of model results to the parameterizations of the atmospheric model is assessed considering the ten most significant recent meteotsunami events for which observations are available. Different schemes adapted to high-resolution Weather Research and Forecasting model simulations were used for the representation of cumulus, microphysics, planetary boundary layer and longwave and shortwave radiations. Results indicate a large spread of the ensemble simulations in terms of the final magnitude of the meteotsunamis. While the modeling system is shown to be able to realistically trigger tsunamigenic atmospheric disturbances in more than 90% of the situations, the small-scale characteristics of these disturbances are significantly modified with the change of parameterizations, leading to significant differences in the magnitude of the simulated sea-level response. No preferred set of parameterizations can be identified that leads to either the largest or the most realistic magnitudes in the majority of situations. Instead, the performance of a given set of parameterizations is found to change with the meteotsunami event under consideration. Importantly, the observed magnitude of the extreme sea-level oscillations lies within the range of a nine-member ensemble in 70% of the cases. This ensemble approach would then allow to generate a realistic range of possibilities in the majority of events, thus improving the realism of meteotsunami predictions compared to single deterministic forecasts. Ključne besede: meteotsunamis prediction, atmosphere, ocean modeling, ensemble forecasting, atmospheric model parameterizations Objavljeno v DiRROS: 19.07.2024; Ogledov: 144; Prenosov: 127
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692. Metagenomic characterization of parental and production CHO cell lines for detection of adventitious virusesKatarina Bačnik, Denis Kutnjak, Barbara Jerič Kokelj, Nika Tuta, Tan Lončar, Matjaž Vogelsang, Maja Ravnikar, 2021, izvirni znanstveni članek Povzetek: Viral contamination is a major concern for biological products. Therefore, virus testing of raw materials and cells is essential for the safety of the final product. We used high-throughput sequencing to detect viral-like sequences in selected CHO cell lines. Our aim was to test various approaches of sample preparation, to establish a pipeline for metagenomic analysis and to characterize standard viral metagenome of production and parental CHO cell lines. The comparison of the metagenomics composition of the differently prepared samples showed that among four tested approaches sequencing of ribosomal RNA depleted total RNA is the most promising approach. The metagenomics investigation of one production and three parental CHO cell lines of diverse origin did not indicate the presence of adventitious viral agents in the investigated samples. The study revealed an expected background of virus-like nucleic acids in the samples, which originate from remains of expression vectors, endogenized viral elements and residuals of bacteriophages. Objavljeno v DiRROS: 19.07.2024; Ogledov: 271; Prenosov: 98
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693. Hepatocellular carcinoma (HepG2/C3A) cell-based 3D model for genotoxicity testing of chemicalsMartina Štampar, Helle Frandsen, Adelina Rogowska-Wrzesinska, Krzysztof Wrzesinski, Metka Filipič, Bojana Žegura, 2021, izvirni znanstveni članek Povzetek: The major weakness of the current in vitro genotoxicity test systems is the inability of the indicator cells to express metabolic enzymes needed for the activation and detoxification of genotoxic compounds, which consequently can lead to misleading results. Thus, there is a significant emphasis on developing hepatic cell models, including advanced in vitro three-dimensional (3D) cell-based systems, which better imitate in vivo cell behaviour and offer more accurate and predictive data for human exposures. In this study, we developed an approach for genotoxicity testing with 21-day old spheroids formed from human hepatocellular carcinoma cells (HepG2/C3A) using the dynamic clinostat bioreactor system (CelVivo BAM/bioreactor) under controlled conditions. The spheroids were exposed to indirect-acting genotoxic compounds, polycyclic aromatic hydrocarbon [PAH; benzo(a) pyrene B(a)P], and heterocyclic aromatic amine [PhIP]) at non-cytotoxic concentrations for 24 and 96 h. The results showed that both environmental pollutants B(a)P and PhIP significantly increased the level of DNA strand breaks assessed by the comet assay. Further, the mRNA level of selected genes encoding metabolic enzymes from phase I and II, and DNA damage responsive genes was determined (qPCR). The 21-day old spheroids showed higher basal expression of genes encoding metabolic enzymes compared to monolayer culture. In spheroids, B(a)P or PhIP induced compound-specific up-regulation of genes implicated in their metabolism, and deregulation of genes implicated in DNA damage and immediate-early response. The study demonstrated that this model utilizing HepG2/C3A spheroids grown under dynamic clinostat conditions represents a very sensitive and promising in vitro model for genotoxicity and environmental studies and can thus significantly contribute to a more reliable assessment of genotoxic activities of pure chemicals, and complex environmental samples even at very low for environmental exposure relevant concentrations. Ključne besede: in vitro 3D cell model, 21-day old spheroids, cytotoxic, genotoxic, gene expression Objavljeno v DiRROS: 19.07.2024; Ogledov: 132; Prenosov: 165
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694. Production of volatile moth sex pheromones in transgenic Nicotiana benthamiana plantsRubèn Mateos Fernández, Elena Moreno Gimenéz, Silvia Gianoglio, Alfredo Quijano-Rubio, Jose Gavaldá-García, Lucía Estellés, Alba Rubert, José Luis Rambla, Marta Vazquez-Vilar, Estefanía Huet, Asunción Fernández-del-Carmen, Ana Espinosa-Ruiz, Mojca Juteršek, Sandra Vacas, Ismael Navarro Fuertes, Vicente Navarro-Llopis, Jaime Primo, Diego Orzaez, 2021, izvirni znanstveni članek Povzetek: Plant-based bioproduction of insect sex pheromones has been proposed as an innovative strategy to increase the sustainability of pest control in agriculture. Here, we describe the engineering of transgenic plants producing (Z)-11-hexadecenol (Z11-16OH) and (Z)-11-hexadecenyl acetate (Z11-16OAc), two main volatile components in many Lepidoptera sex pheromone blends. We assembled multigene DNA constructs encoding the pheromone biosynthetic pathway and stably transformed them into Nicotiana benthamiana plants. The constructs contained the Amyelois transitella AtrΔ11 desaturase gene, the Helicoverpa armigera fatty acyl reductase HarFAR gene, and the Euonymus alatus diacylglycerol acetyltransferase EaDAct gene in different configurations. All the pheromone-producing plants showed dwarf phenotypes, the severity of which correlated with pheromone levels. All but one of the recovered lines produced high levels of Z11-16OH, but very low levels of Z11-16OAc, probably as a result of recurrent truncations at the level of the EaDAct gene. Only one plant line (SxPv1.2) was recovered that harboured an intact pheromone pathway and which produced moderate levels of Z11-16OAc (11.8 μg g-1 FW) and high levels of Z11-16OH (111.4 μg g-1). Z11-16OAc production was accompanied in SxPv1.2 by a partial recovery of the dwarf phenotype. SxPv1.2 was used to estimate the rates of volatile pheromone release, which resulted in 8.48 ng g-1 FW per day for Z11-16OH and 9.44 ng g-1 FW per day for Z11-16OAc. Our results suggest that pheromone release acts as a limiting factor in pheromone biodispenser strategies and establish a roadmap for biotechnological improvements. Objavljeno v DiRROS: 19.07.2024; Ogledov: 288; Prenosov: 138
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695. A mini-TGA protein modulates gene expression through heterogeneous association with transcription factorsŠpela Tomaž, Marko Petek, Tjaša Lukan, Karmen Pogačar, Katja Stare, Erica Teixeira Prates, Daniel A. Jacobson, Jan Zrimec, Gregor Bajc, Matej Butala, Maruša Pompe Novak, Ajda Taler-Verčič, Aleksandra Usenik, Dušan Turk, Anna Coll Rius, Kristina Gruden, 2022, izvirni znanstveni članek Povzetek: TGA (TGACG-binding) transcription factors, which bind their target DNA through a conserved basic region leucine zipper (bZIP) domain, are vital regulators of gene expression in salicylic acid (SA)-mediated plant immunity. Here, we investigated the role of StTGA2.1, a potato (Solanum tuberosum) TGA lacking the full bZIP, which we named a mini-TGA. Such truncated proteins have been widely assigned as loss-of-function mutants. We, however, confirmed that StTGA2.1 overexpression compensates for SA-deficiency, indicating a distinct mechanism of action compared with model plant species. To understand the underlying mechanisms, we showed that StTGA2.1 can physically interact with StTGA2.2 and StTGA2.3, while its interaction with DNA was not detected. We investigated the changes in transcriptional regulation due to StTGA2.1 overexpression, identifying direct and indirect target genes. Using in planta transactivation assays, we confirmed that StTGA2.1 interacts with StTGA2.3 to activate StPRX07, a member of class III peroxidases (StPRX), which are known to play role in immune response. Finally, via structural modeling and molecular dynamics simulations, we hypothesized that the compact molecular architecture of StTGA2.1 distorts DNA conformation upon heterodimer binding to enable transcriptional activation. This study demonstrates how protein truncation can lead to distinct functions and that such events should be studied carefully in other protein families. Objavljeno v DiRROS: 18.07.2024; Ogledov: 201; Prenosov: 100
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696. Hyperthermia as a potential cornerstone of effective multimodality treatment with radiotherapy, cisplatin and PARP inhibitor in IDH1-mutated cancer cellsMohammed Khurshed, Elia Prades-Sagarra, Sarah Al Saleh, Peter Sminia, Johanna W Wilmink, Remco J. Molenaar, Hans Crezee, Cornelis J. F. van Noorden, 2022, izvirni znanstveni članek Povzetek: Mutations in the isocitrate dehydrogenase 1 (IDH1MUT) gene occur in various types of malignancies, including ~60% of chondrosarcomas, ~30% of intrahepatic cholangiocarcinomas and >80% of low-grade gliomas. IDH1MUT are causal in the development and progression of these types of cancer due to neomorphic production of the oncometabolite D-2-hydroxyglutarate (D-2HG). Intracellular accumulation of D-2HG has been implicated in suppressing homologous recombination and renders IDH1MUT cancer cells sensitive to DNA-repair-inhibiting agents, such as poly-(adenosine 5′-diphosphate–ribose) polymerase inhibitors (PARPi). Hyperthermia increases the efficacy of DNA-damaging therapies such as radiotherapy and platinum-based chemotherapy, mainly by inhibition of DNA repair. In the current study, we investigated the additional effects of hyperthermia (42 °C for 1 h) in the treatment of IDH1MUT HCT116 colon cancer cells and hyperthermia1080 chondrosarcoma cancer cells in combination with radiation, cisplatin and/or a PARPi on clonogenic cell survival, cell cycle distribution and the induction and repair of DNA double-strand breaks. We found that hyperthermia in combination with radiation or cisplatin induces an increase in double-strand breaks and cell death, up to 10-fold in IDH1MUT cancer cells compared to IDH1 wild-type cells. This vulnerability was abolished by the IDH1MUT inhibitor AGI-5198 and was further increased by the PARPi. In conclusion, our study shows that IDH1MUT cancer cells are sensitized to hyperthermia in combination with irradiation or cisplatin and a PARPi. Therefore, hyperthermia may be an efficacious sensitizer to cytotoxic therapies in tumors where the clinical application of hyperthermia is feasible, such as IDH1MUT chondrosarcoma of the extremities. Ključne besede: isocitrate dehydrogenase, PARP, hyperthermia, D‐2‐hydroxyglutarate, radiotherapy, cisplatin Objavljeno v DiRROS: 18.07.2024; Ogledov: 199; Prenosov: 156
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697. Towards better-informed dispersal probabilities in historical biogeography : arachnids as a model lineageMatjaž Kuntner, Eva Turk, 2022, izvirni znanstveni članek Povzetek: Historical biogeography is an integrative scientific field critical for testing evolutionary hypotheses pertinent to organismal distributions, but despite recent theoretical and analytical advances, biogeographic reconstructions continue to struggle with accuracy and rigor. Most modern studies include the three elements needed for historical biogeographic inference, namely a time-calibrated phylogeny, contemporary taxonomic distributions, and estimations of organismal dispersal probabilities. The latter, we argue, are particularly vague, and historical biogeography would greatly benefit from dispersal probability estimations that are better informed and biologically meaningful. To achieve that goal, next-generation biogeography should ideally consider: a) dispersal-related traits; b) ecology; c) geological histories; and d) geographical factors. We briefly recap the three case studies on spiders that have pioneered this approach. Due to their old age and mega-diversity—considering both phylogenetic and life style diversity—arachnids are an ideal animal lineage for modern biogeographic research. There is no reason, however, that the concept should not be applied to all life. Further modifications of the proposed concept and, particularly, methodological implementation are needed to render this biogeographic framework widely useful. Ključne besede: next-generation biogeography, ancestral areas, dispersal biology, geological history, vicariance, extinction, arachnids Objavljeno v DiRROS: 18.07.2024; Ogledov: 152; Prenosov: 89
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698. Multi-platform study of the extreme bloom of the barrel jellyfish Rhizostoma pulmo (Cnidaria: Scyphozoa) in the northernmost gulf of the Mediterranean Sea (Gulf of Trieste) in April 2021Nydia Catalina Reyes Suárez, Valentina Tirelli, Laura Ursella, Matjaž Ličer, Massimo Celio, Vanessa Cardin, 2022, izvirni znanstveni članek Povzetek: On 7 April 2021, an exceptional bloom of the scyphomedusa Rhizostoma pulmo was observed in the Gulf of Trieste (Italy). Blooms of this species in the northern Adriatic Sea have been reported since the late 1800s: the density of jellyfish observed in 2021 reached more than 10 specimens per square metre. We analyse the bloom from a multi-platform approach using observations and model data at different timescales. We attempt to explain the intensity of the bloom as a consequence of thermohaline and hydrodynamical conditions in the gulf. Meteo-oceanographic conditions that may have contributed to the exceptional aggregation of jellyfish observed along the northernmost coast of the Adriatic Sea are discussed in detail. Specifically, our results indicate that this bloom was enabled by (1) the presence of a high number of jellyfish in the gulf, probably linked to the anomalously warm sea conditions in spring 2020 and winter 2021, which may have favoured a longer reproductive period and enhanced survival of adult R. pulmo, respectively; and (2) strong wind events, such as the bora wind for the Gulf of Trieste, which enhanced upwelling and mixing processes in the gulf, bringing the jellyfish from the deeper waters to the surface and clustering them along the coast. Ključne besede: jellyfishes, Gulf of Trieste, Mediterranean Sea, hydrobiology, marine biology Objavljeno v DiRROS: 18.07.2024; Ogledov: 166; Prenosov: 127
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699. First application of the AMBI index to the macrobenthic soft-bottom community of Terra Nova Bay (Ross Sea, Southern Ocean)Cristina Munari, Ángel Borja, Cinzia Corinaldesi, Eugenio Rastelli, Marco Lo Martire, Valentina Pitacco, Michele Mistri, 2022, izvirni znanstveni članek Povzetek: The assemblages of marine benthic organisms and sediment characteristics were investigated in the coastal area between the Mario Zucchelli Antarctic Research Station and Adelie Cove in Terra Nova Bay (Ross Sea, Southern Ocean) during the 2015 summer season. Sediment samples were taken from 11 stations at depths between 25 and 140 m. The dominance of sand characterised sites, and the biochemical composition of the sedimentary organic matter resulted in very variable between the different sites. A total of 142 taxa were identified, with Annelida (68 taxa) and Arthropoda (35 taxa) constituting the main macrobenthic groups. The benthic community at deeper stations showed higher species richness and lower dominance compared to the shallower stations. For the first time in Antarctica, we also investigated the response of the AZTI’s Marine Biotic Index (AMBI) to the organic gradient. Of the 142 taxa found, 97 were not listed in the AMBI library, and we were able to assign as many as 88 taxa to an ecological group. All of these new species were added to the new AMBI species list. AMBI showed a good response to the organic gradient. Ključne besede: antarctic benthos, ecological quality assessment, indexes, Ross Sea Objavljeno v DiRROS: 18.07.2024; Ogledov: 172; Prenosov: 167
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700. Expression of inducible factors reprograms CAR-T cells for enhanced function and safetyAnže Smole, Alexander Benton, Mathilde A. Poussin, Monika A. Eiva, Claudia Mezzanotte, 2022, izvirni znanstveni članek Povzetek: Despite the success of CAR-T cell cancer immunotherapy, challenges in efficacy and safety remain. Investigators have begun to enhance CAR-T cells with the expression of accessory molecules to address these challenges. Current systems rely on constitutive transgene expression or multiple viral vectors, resulting in unregulated response and product heterogeneity. Here, we develop a genetic platform that combines autonomous antigen-induced production of an accessory molecule with constitutive CAR expression in a single lentiviral vector called Uni-Vect. The broad therapeutic application of Uni-Vect is demonstrated in vivo by activation-dependent expression of (1) an immunostimulatory cytokine that improves efficacy, (2) an antibody that ameliorates cytokine-release syndrome, and (3) transcription factors that modulate T cell biology. Uni-Vect is also implemented as a platform to characterize immune receptors. Overall, we demonstrate that Uni-Vect provides a foundation for a more clinically actionable next-generation cellular immunotherapy. Ključne besede: CAR-T cells, TCR, inducible, transcription factor, NFAT, single lentiviral expression system, IL-6, IL-12, CRS, armored Objavljeno v DiRROS: 18.07.2024; Ogledov: 201; Prenosov: 37
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