1291. 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: 318; Downloads: 268
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1292. 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: 260; Downloads: 177
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1293. 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: 328; Downloads: 237
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1294. 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: 271; Downloads: 196
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1295. 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: 315; Downloads: 956
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1296. 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: 278; Downloads: 189
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1297. Scyphomedusae and Ctenophora of the Eastern Adriatic : historical overview and new dataBranka Pestorić, Davor Lučić, Natalia Bojanić, Martin Vodopivec, Tjaša Kogovšek, Ivana Violić, Paolo Paliaga, Alenka Malej, 2021, original scientific article Abstract: One of the obstacles to detecting regional trends in jellyfish populations is the lack of a defined baseline. In the Adriatic Sea, the jellyfish fauna (Scyphozoa and Ctenophora) is poorly studied compared to other taxa. Therefore, our goal was to collect and systematize all available data and provide a baseline for future studies. Here we present phenological data and relative abundances of jellyfish based on 2010–2019 scientific surveys and a “citizen science” sighting program along the eastern Adriatic. Inter-annual variability, seasonality and spatial distribution patterns of Scyphomedusae and Ctenophore species were described and compared with existing historical literature. Mass occurrences with a clear seasonal pattern and related to the geographical location were observed for meroplanktonic Scyphomedusae Aurelia solida, Rhizostoma pulmo, and to a lesser extent Chrysaora hysoscella, Cotylorhiza tuberculata and Discomedusa lobata. Holoplanktonic Pelagia noctiluca also formed large aggregations, which were seasonally less predictable and restricted to the central and southern Adriatic. Four species of Ctenophora produced blooms limited to a few areas: Bolinopsis vitrea, Leucothea multicornis, Cestum veneris and the non-native Mnemiopsis leidyi. However, differences between Adriatic subregions have become less pronounced since 2014. Our results suggest that gelatinous organisms are assuming an increasingly important role in the Adriatic ecosystem, which may alter the balance of the food web and lead to harmful and undesirable effects.
Keywords: jellyfish phenology, hydrobiology, long-term changes, Mediterranean Sea
Published in DiRROS: 19.07.2024; Views: 306; Downloads: 205
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1298. The role of heparan sulfate and neuropilin 2 in VEGFA signaling in human endothelial tip cells and non-tip cells during angiogenesis in vitroMarchien G. Dallinga, Yasmin I. Habani, Alinda W. M. Schimmel, Geesje M. Dallinga-Thie, Cornelis J. F. van Noorden, Ingeborg Klaassen, Reinier O. Schlingemann, 2021, original scientific article Abstract: During angiogenesis, vascular endothelial growth factor A (VEGFA) regulates endothelial cell (EC) survival, tip cell formation, and stalk cell proliferation via VEGF receptor 2 (VEGFR2). VEGFR2 can interact with VEGFR2 co-receptors such as heparan sulfate proteoglycans (HSPGs) and neuropilin 2 (NRP2), but the exact roles of these co-receptors, or of sulfatase 2 (SULF2), an enzyme that removes sulfate groups from HSPGs and inhibits HSPG-mediated uptake of very low density lipoprotein (VLDL), in angiogenesis and tip cell biology are unknown. In the present study, we investigated whether the modulation of binding of VEGFA to VEGFR2 by knockdown of SULF2 or NRP2 affects sprouting angiogenesis, tip cell formation, proliferation of non-tip cells, and EC survival, or uptake of VLDL. To this end, we employed VEGFA splice variant 121, which lacks an HSPG binding domain, and VEGFA splice variant 165, which does have this domain, in in vitro models of angiogenic tip cells and vascular sprouting. We conclude that VEGFA165 and VEGFA121 have similar inducing effects on tip cells and sprouting in vitro, and that the binding of VEGFA165 to HSPGs in the extracellular matrix does not seem to play a role, as knockdown of SULF2 did not alter these effects. Co-binding of NRP2 appears to regulate VEGFA–VEGFR2-induced sprout initiation, but not tip cell formation. Finally, as the addition of VLDL increased sprout formation but not tip cell formation, and as VLDL uptake was limited to non-tip cells, our findings suggest that VLDL plays a role in sprout formation by providing biomass for stalk cell proliferation.
Keywords: endothelial cells, angiogenesis, VEGFA, tip cells, SULF2, NRP2, HSPG
Published in DiRROS: 19.07.2024; Views: 255; Downloads: 200
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1299. Multi-platform, high-resolution study of a complex coastal system : the TOSCA experiment in the Gulf of TriesteStefano Querin, Simone Cosoli, Riccardo Gerin, Célia Laurent, Vlado Malačič, Neva Pristov, Pierre-Marie Poulain, 2021, original scientific article Abstract: Abstract
Although small in size, the Gulf of Trieste (GoT), a marginal coastal basin in the northern Adriatic Sea, is characterized by very complex dynamics and strong variability of its oceanographic conditions. In April–May 2012, a persistent, large-scale anticyclonic eddy was observed in the GoT. This event was captured by both High Frequency Radar (HFR) and Lagrangian drifter observations collected within the European MED TOSCA (Tracking Oil Spill and Coastal Awareness) project. The complexity of the system and the variety of forcing factors constitute major challenges from a numerical modeling perspective when it comes to simulating the observed features. In this study, we implemented a high-resolution hydrodynamic model in an attempt to reproduce and analyze the observed basin-wide eddy structure and determine its drivers. We adopted the Massachusetts Institute of Technology General Circulation Model (MITgcm), tailored for the GoT, nested into a large-scale simulation of the Adriatic Sea and driven by a tidal model, measured river freshwater discharge data and surface atmospheric forcing. Numerical results were qualitatively and quantitatively evaluated against HFR surface current maps, Lagrangian drifter trajectories and thermohaline data, showing good skills in reproducing the general circulation, but failing in accurately tracking the drifters. Model sensitivity to different forcing factors (wind, river and tides) was also assessed.
Keywords: Adriatic Sea, surface circulation, HF coastal radars, Lagrangian drifters, wind-driven currents, ocean circulation models
Published in DiRROS: 19.07.2024; Views: 306; Downloads: 215
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1300. Detection of four new tomato viruses in Serbia using post hoc high-throughput sequencing analysis of samples from a large-scale field surveyAna Vučurović, Denis Kutnjak, Nataša Mehle, Ivana Stanković, Anja Pecman, Aleksandra Bulajić, Branka Krstić, Maja Ravnikar, 2021, original scientific article Abstract: Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.
Keywords: viruses, tomato, detection, identification
Published in DiRROS: 19.07.2024; Views: 351; Downloads: 268
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