661. Biochemical and functional characterization of mutant KRAS epitopes validates this oncoprotein for immunological targeting.Adham S. Bear, Tatiana Blanchardt, Joseph Cesare, Michael J. Ford, Lee P. Richman, Chong Xu, Miren L. Baroja, Sarah McCuaig, Christina Costeas, Khatuna Gabunia, John Scholler, Avery D. Posey, Mark H. OʹHara, Anže Smole, Daniel J. Powell, Benjamin A. Garcia, Robert H. Vonderheide, Gerald P. Linette, Beatriz M Carreno, 2021, original scientific article Abstract: Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here we employ a multi-omics approach to characterize HLA class I-restricted mKRAS epitopes. We provide proteomic evidence of mKRAS epitope processing and presentation by high prevalence HLA class I alleles. Select epitopes are immunogenic enabling mKRAS-specific TCRαβ isolation. TCR transfer to primary CD8+ T cells confers cytotoxicity against mKRAS tumor cell lines independent of histologic origin, and the kinetics of lytic activity correlates with mKRAS peptide-HLA class I complex abundance. Adoptive transfer of mKRAS-TCR engineered CD8+ T cells leads to tumor eradication in a xenograft model of metastatic lung cancer. This study validates mKRAS peptides as bona fide epitopes facilitating the development of immune therapies targeting this oncoprotein. Published in DiRROS: 19.07.2024; Views: 102; Downloads: 105
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662. Sequestration of polystyrene microplastics by jellyfish mucusŽiva Lengar, Katja Klun, Iztok Dogša, Ana Rotter, David Stopar, 2021, original scientific article Abstract: The worldwide microplastics pollution is a serious environmental and health problem that is currently not effectively mitigated. In this work we tested jellyfish mucus as a new bioflocculent material capable of sequestration of polystyrene microplastics in aqueous environments. Mucus material was collected from different jellyfish species and was used to trap fluorescently tagged polystyrene microspheres. The efficiency of removal was tested using varying concentrations of microplastics and mucus. The interaction between the microplastics and mucus was determined by viscosity measurements and confocal laser scanning microscopy. Different mucus preparation methods were also tested: freshly prepared, mechanically sheared, freeze-thawed, freeze-dried, and hydrolyzed mucus. The results demonstrate that jellyfish mucus can efficiently sequester polystyrene microplastics particles from the suspension. The fraction of the removed microplastics was highest with freshly prepared mucus and decreased with freeze-thawing and freeze-drying. The mucus ability to sequester microplastics was completely lost in the hydrolyzed mucus. The results imply that the intact jellyfish mucus has the potential to be used as a biopolymer capable of removing microplastics material. Published in DiRROS: 19.07.2024; Views: 120; Downloads: 130
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663. Comparison of in-situ chlorophyll-a time series and sentinel-3 ocean and land color instrument data in Slovenian national waters (Gulf of Trieste, Adriatic Sea)El Khalil Cherif, Patricija Mozetič, Janja Francé, Vesna Flander-Putrle, Jana Faganeli Pucer, Martin Vodopivec, 2021, original scientific article Abstract: While satellite remote sensing of ocean color is a viable tool for estimating large-scale patterns of chlorophyll-a (Chl-a) and global ocean primary production, its application in coastal waters is limited by the complex optical properties. An exploratory study was conducted in the Gulf of Trieste (Adriatic Sea) to assess the usefulness of Sentinel-3 satellite data in the Slovenian national waters. OLCI (Ocean and Land Colour Instrument) Chl-a level 2 products (OC4Me and NN) were compared to monthly Chl-a in-situ measurements at fixed sites from 2017 to 2019. In addition, eight other methods for estimating Chl-a concentration based on reflectance in different spectral bands were tested (OC3M, OC4E, MedOC4, ADOC4, AD4, 3B-OLCI, 2B-OLCI and G2B). For some of these methods, calibration was performed on in-situ data to achieve a better agreement. Finally, L1-regularized regression and random forest were trained on the available dataset to test the capabilities of the machine learning approach. The results show rather poor performance of the two originally available products. The same is true for the other eight methods and the fits to the measured values also show only marginal improvement. The best results are obtained with the blue-green methods (OC3, OC4 and AD4), especially the AD4SI (a designated fit of AD4) with R = 0.56 and RMSE = 0.4 mg/m³, while the near infrared (NIR) methods show underwhelming performance. The machine learning approach can only explain 30% of the variability and the RMSE is of the same order as for the blue-green methods. We conclude that due to the low Chl-a concentration and the moderate turbidity of the seawater, the reflectance provided by the Sentinel-3 OLCI spectrometer carries little information about Chl-a in the Slovenian national waters within the Gulf of Trieste and is therefore of limited use for our purposes. This requires that we continue to improve satellite products for use in those marine waters that have not yet proven suitable. In this way, satellite data could be effectively integrated into a comprehensive network that would allow a reliable assessment of ecological status, taking into account environmental regulations. Keywords: hydrobiology, coastal waters, Gulf of Trieste, chlorophyll-a, Sentinel-3, OLCI, machine learning Published in DiRROS: 19.07.2024; Views: 123; Downloads: 590
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664. The pathogens spillover and incidence correlation in bumblebees and honeybees in SloveniaMetka Pislak, Ivan Toplak, Urška Zajc, Danilo Bevk, 2021, original scientific article Abstract: Slovenia has a long tradition of beekeeping and a high density of honeybee colonies, but less is known about bumblebees and their pathogens. Therefore, a study was conducted to define the incidence and prevalence of pathogens in bumblebees and to determine whether there are links between infections in bumblebees and honeybees. In 2017 and 2018, clinically healthy workers of bumblebees (Bombus spp.) and honeybees (Apis mellifera) were collected on flowers at four different locations in Slovenia. In addition, bumblebee queens were also collected in 2018. Several pathogens were detected in the bumblebee workers using PCR and RT-PCR methods: 8.8% on acute bee paralysis virus (ABPV), 58.5% on black queen cell virus (BQCV), 6.8% on deformed wing virus (DWV), 24.5% on sacbrood bee virus (SBV), 15.6% on Lake Sinai virus (LSV), 16.3% on Nosema bombi, 8.2% on Nosema ceranae, 15.0% on Apicystis bombi and 17.0% on Crithidia bombi. In bumblebee queens, only the presence of BQCV, A. bombi and C. bombi was detected with 73.3, 26.3 and 33.3% positive samples, respectively. This study confirmed that several pathogens are regularly detected in both bumblebees and honeybees. Further studies on the pathogen transmission routes are required. Published in DiRROS: 19.07.2024; Views: 104; Downloads: 82
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665. A review of constraints and solutions for collecting raptor samples and contextual data for a European Raptor Biomonitoring FacilityMaria Dulsat-Masvidal, Rui Lorenço, Silvia Lacorte, Tamer Albayarak, Marcello DʹAmico, Jovan Andevski, Al Vrezec, Arianna Aradis, Emanuel Baltag, Oded Berger-Tal, 2021, original scientific article Abstract: The COST Action ‘European Raptor Biomonitoring Facility’ (ERBFacility) aims to develop pan-European raptor biomonitoring in support of better chemicals management in Europe, using raptors as sentinel species. This presents a significant challenge involving a range of constraints that must be identified and addressed. The aims of this study were to: (1) carry out a comprehensive review of the constraints that may limit the gathering in the field of raptor samples and contextual data, and assess their relative importance across Europe; and (2) identify and discuss possible solutions to the key constraints that were identified. We applied a participatory approach to identify constraints and to discuss feasible solutions. Thirty-one constraints were identified, which were divided into four categories: legal, methodological, spatial coverage, and skills constraints. To assess the importance of the constraints and their possible solutions, we collected information through scientific workshops and by distributing a questionnaire to stakeholders in all the countries involved in ERBFacility. We obtained 74 answers to the questionnaire, from 24 of the 39 COST participating countries. The most important constraints identified were related to the collection of complex contextual data about sources of contamination, and the low number of existing raptor population national/regional monitoring schemes and ecological studies that could provide raptor samples. Legal constraints, such as permits to allow the collection of invasive samples, and skills constraints, such as the lack of expertise to practice necropsies, were also highlighted. Here, we present solutions for all the constraints identified, thus suggesting the feasibility of establishing a long-term European Raptor Sampling Programme as a key element of the planned European Raptor Biomonitoring Facility. Published in DiRROS: 19.07.2024; Views: 107; Downloads: 131
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666. Systems toxicology approach for assessing developmental neurotoxicity in Larval zebrafishRoman Li, Marja Talikka, Vincenzo Belcastro, Colette vom Berg, Florian Martin, Manuel C. Peitsch, Julia Hoeng, Anže Županič, 2021, original scientific article Abstract: Adverse outcomes that result from chemical toxicity are rarely caused by dysregulation of individual proteins; rather, they are often caused by system-level perturbations in networks of molecular events. To fully understand the mechanisms of toxicity, it is necessary to recognize the interactions of molecules, pathways, and biological processes within these networks. The developing brain is a prime example of an extremely complex network, which makes developmental neurotoxicity one of the most challenging areas in toxicology. We have developed a systems toxicology method that uses a computable biological network to represent molecular interactions in the developing brain of zebrafish larvae. The network is curated from scientific literature and describes interactions between biological processes, signaling pathways, and adverse outcomes associated with neurotoxicity. This allows us to identify important signaling hubs, pathway interactions, and emergent adverse outcomes, providing a more complete understanding of neurotoxicity. Here, we describe the construction of a zebrafish developmental neurotoxicity network and its validation by integration with publicly available neurotoxicity-related transcriptomic datasets. Our network analysis identified consistent regulation of tumor suppressors p53 and retinoblastoma 1 (Rb1) as well as the oncogene Krüppel-like factor (Klf8) in response to chemically induced developmental neurotoxicity. The developed network can be used to interpret transcriptomic data in a neurotoxicological context. Published in DiRROS: 19.07.2024; Views: 126; Downloads: 100
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667. Observations on the surface structure of Aurelia solida (Scyphozoa) polyps and medusaeValentina Turk, Ana Fortič, Maja Kos Kramar, Magda Tušek-Žnidarič, Jasna Štrus, Rok Kostanjšek, Alenka Malej, 2021, original scientific article Abstract: The surface structures and mucus layers that form an interface between the epithelial layer of organisms and their external environment were studied in the bloom-forming moon jellyfish (Aurelia solida, Scyphozoa) from the northern Adriatic. The surface of the polyps revealed epithelial ciliated cells and numerous nematocysts, both non-discharged and discharged. Cilia were also the most prominent features on the surface of adult medusa, protruding from the epidermal cells and with microvilli surrounding the base. Histochemical methods and various microscopy techniques (light/epifluorescence and electron microscopy) confirmed the presence of abundant mucus around polyps and on the surfaces of adult medusa, and that the mucus contained acidic and neutral mucins. The observed mucus secretions on the exumbrella surface of the medusae were in the form of granules, flocs, and sheets. Scanning electron microscopy and transmission electron microscopy analyses confirmed the presence of various microbes in the mucus samples, but not on the epithelial surfaces of the polyps or the exumbrella of the medusae. Published in DiRROS: 19.07.2024; Views: 152; Downloads: 124
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668. Sediment contamination by heavy metals and PAH in the Piombino channel (Tyrrhenian sea)Valentina Pitacco, Michele Mistri, Tommaso Granata, Letizia Moruzzi, Maria Laura Meloni, Francesca Massara, Adriano Sfriso, Andrea Augusto Sfriso, Cristina Munari, 2021, original scientific article Abstract: Sediment contamination is of major concern in areas affected by heavy maritime traffic. The spatial variation and contamination of 11 trace elements and 17 PAHs in surface sediments were studied along a 31 km transect along the seaway from the port of Piombino (Tuscany) to the port of Portoferraio (Elba Island) in the Northern Tyrrhenian Sea. Heavy metal contamination was detected at sites near Piombino (Ni, Pb, Hg, Cu and Zn) and at sites near Portoferraio (Pb, Zn, Hg, Cr and Cd). Each of the 35 sampled sites showed PAH contamination, with the highest concentrations at sites near Portoferraio. The most abundant isomers detected were 2- and 4-ring PAHs. PAH ratio analysis showed a prevalence of PAHs of pyrolytic origin. High values of PAHs and heavy metals were related to high sediment water content, TOC, silt, and clay content. Arsenic increased with increasing depth. The correlation between concentrations of metals and PAHs suggests common anthropogenic sources and is of concern for possible synergistic adverse effects on the biota. Published in DiRROS: 19.07.2024; Views: 104; Downloads: 104
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669. Prunus persica plant endogenous peptides PpPep1 and PpPep2 cause PTI-like transcriptome reprogramming in peach and enhance resistance to Xanthomonas arboricola pv. pruniLaura Foix, Anna Nadal, Maja Zagorščak, Živa Ramšak, Anna Esteve-Godina, Kristina Gruden, Maria Pla, 2021, original scientific article Abstract: Background
Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which are of them being plant elicitor peptides (Peps). Exogenous application of Peps activates defense mechanisms and reduces the symptoms of pathogen infection in various pathosystems. We have previously identified the Rosaceae Peps and showed, in an ex vivo system, that their topical application efficiently enhanced resistance to the bacterial pathogen Xanthomonas arboricola pv. pruni (Xap).
Results
Here we demonstrate the effectiveness of Prunus persica peptides PpPep1 and PpPep2 in protecting peach plants in vivo at nanomolar doses, with 40% reduction of the symptoms following Xap massive infection. We used deep sequencing to characterize the transcriptomic response of peach plants to preventive treatment with PpPep1 and PpPep2. The two peptides induced highly similar massive transcriptomic reprogramming in the plant. One hour, 1 day and 2 days after peptide application there were changes in expression in up to 8% of peach genes. We visualized the transcriptomics dynamics in a background knowledge network and detected the minor variations between plant responses to PpPep1 and PpPep2, which might explain their slightly different protective effects. By designing a P. persica Pep background knowledge network, comparison of our data and previously published immune response datasets was possible.
Conclusions
Topical application of P. persica Peps mimics the PTI natural response and protects plants against massive Xap infection. This makes them good candidates for deployment of natural, targeted and environmental-friendly strategies to enhance resistance in Prunus species and prevent important biotic diseases. Published in DiRROS: 19.07.2024; Views: 154; Downloads: 885
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670. Temporal changes of a fouling community: colonization patterns of the benthic epifauna in the shallow northern Adriatic SeaAna Fortič, Borut Mavrič, Valentina Pitacco, Lovrenc Lipej, 2021, original scientific article Abstract: Sessile benthic communities are an important element of marine ecosystems, yet their temporal patterns remain poorly understood. For this reason, the temporal changes of the fouling community on brick plates in Piran Bay, Gulf of Trieste (northern Adriatic Sea), were studied for two calendar years. The aim of this study was to identify the settlement of dominant native and alien species on artificial substrates and their temporal occurrence, both in terms of season and duration of submersion. In addition, we tried to assess the impact of the placement period on developing communities. The dominant taxonomic groups were bryozoans, which accounted for almost half of the total coverage (46%), serpulid polychaetes (25%) and bivalves (11%). Most of the species belonging to the dominant taxa occurred throughout the year, with the peak of occurrence in summer. The first settlers included serpulids and bivalves, which were constantly found on the plates together with bryozoans. Alien and cryptogenic species represented about 13% of all taxa found during the study. This highlights the importance of bare artificial structures erected outside typical hotspots for alien species; they serve as a springboard for the spread of alien fouling species. The communities that formed on plates placed in different seasons showed significant differences between them. High bryozoan coverage characterized the communities placed in winter and spring, while the plates placed in summer and autumn were dominated by serpulid polychaetes. These differences are the result of species seasonality as well as the interaction between them. The study demonstrates the importance of timing for initial colonization. It can be linked to the placement of the bare substrate for the development of the community, and provides a baseline for research and projects involving underwater constructions and the detection of alien species. Published in DiRROS: 19.07.2024; Views: 113; Downloads: 122
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