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12. An insight into the feeding ecology of Serranus Scriba, a Shallow water mesopredator in the Northern Adriatic Sea, with a non-destructive methodAna Lokovšek, Martina Orlando-Bonaca, Domen Trkov, Lovrenc Lipej, 2022, original scientific article Abstract: Serranus scriba is a common member of the coastal fish community in the Adriatic Sea, but knowledge about its feeding ecology is scarce. The aim of this paper is to present new evidence about its food preferences and feeding habits. An innovative non-destructive method of fecal pellet analysis was used for this study. This method does not require sacrificing specimens and the fish can be released back into the sea alive after the laboratory work. The results demonstrated that S. scriba mainly preys on decapods, followed by polychaetes, isopods, fish, mollusks and swarming shrimps. The calculated index of trophic diversity (ITD) value of 0.89 indicates that it is an opportunistic feeder that feeds on a wide range of different prey. According to the calculated trophic level of 3.43, which is higher than that of other members of the community, S. scriba is also an important piscivorous predator. With age, S. scriba undergoes an ontogenetic shift. The proportion of crustaceans, gastropods and polychaetes decreases with age and body size, while the proportion of fish increases.
Keywords: coastal fishes, diet, non-destructive method, non-lethal method, painted comber, northern Adriatic
Published in DiRROS: 17.07.2024; Views: 1; Downloads: 0
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13. Evaluation of methods and processes for robust monitoring of SARS-CoV-2 in wastewaterOlivera Maksimović, Živa Lengar, Zala Kogej Zwitter, Katarina Bačnik, Irena Bajde, Mojca Milavec, Anže Županič, Nataša Mehle, Denis Kutnjak, Maja Ravnikar, Ion Gutiérrez-Aguirre, 2022, original scientific article Abstract: The SARS-CoV-2 pandemic has accelerated the development of virus concentration and molecular-based virus detection methods, monitoring systems and overall approach to epidemiology. Early into the pandemic, wastewater-based epidemiology started to be employed as a tool for tracking the virus transmission dynamics in a given area. The complexity of wastewater coupled with a lack of standardized methods led us to evaluate each step of the analysis individually and see which approach gave the most robust results for SARS-CoV-2 monitoring in wastewater. In this article, we present a step-by-step, retrospective view on the method development and implementation for the case of a pilot monitoring performed in Slovenia. We specifically address points regarding the thermal stability of the samples during storage, screening for the appropriate sample concentration and RNA extraction procedures and real-time PCR assay selection. Here, we show that the temperature and duration of the storage of the wastewater sample can have a varying impact on the detection depending on the structural form in which the SARS-CoV-2 target is present. We found that concentration and RNA extraction using Centricon filtration units coupled with Qiagen RNA extraction kit or direct RNA capture and extraction using semi-automated kit from Promega give the most optimal results out of the seven methods tested. Lastly, we confirm the use of N1 and N2 assays developed by the CDC (USA) as the best performing assays among four tested in combination with Fast Virus 1-mastermix. Data show a realistic overall process for method implementation as well as provide valuable information in regards to how different approaches in the analysis compare to one another under the specific conditions present in Slovenia during a pilot monitoring running from the beginning of the pandemic.
Keywords: waste water, method evolution, virus detection, SARS-CoV-2
Published in DiRROS: 17.07.2024; Views: 0; Downloads: 0
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14. What did we achieve with VALITEST an EU project on validation in plant pest diagnostics?Charlotte Trontin, Barbara Agstner, Denise Altenbach, Géraldine Anthoine, Hanna Baginska, Ian Brittain, A Chabirand, Anne-Marie Chappé, P. Dahlin, Tanja Dreo, C. Freye-Minks, Camilo Gianinazzi, Catherine Harrison, Glyn Jones, Marco Stefan Kaiser, Marta Luigi, Sébastien Massart, Nataša Mehle, Monica Mezzalama, Hanna Mouaziz, Maja Ravnikar, Tom Raaymakers, Jean-Philippe Renvoise, Mathieu Rolland, Marta Santos, Sam Seddas, René van der Vlugt, Ana Vučurović, Françoise Petter, 2022, original scientific article Keywords: plant pest diagnostics, validation, test performance study, high-throughput, sequencing, reference material, training
Published in DiRROS: 17.07.2024; Views: 0; Downloads: 1
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15. Tartary buckwheat flavonoids improve colon lesions and modulate gut microbiota composition in diabetic miceWenwen Cheng, Cifeng Cai, Ivan Kreft, Tamara Lah Turnšek, Mingyan Zu, Yongping Hu, Meiliang Zhou, Zhiyong Liao, 2022, original scientific article Abstract: Tartary buckwheat flavonoids (TBFs) exhibit diverse biological activities, with antioxidant, antidiabetes, anti-inflammatory, and cholesterol-lowering properties. In this study, we investigated the role of TBFs in attenuating glucose and lipid disturbances in diabetic mice and hence preventing the occurrence of diabetes-related colon lesions in mice by regulating the gut microbiota. The results showed that TBFs (1) reversed blood glucose levels and body weight changes; (2) improved levels of serum total cholesterol (TC), triglycerides (TGs), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and fasting insulin; and (3) significantly reduced diabetes-related colon lesions in diabetic mice. In addition, TBFs also affected the diabetes-related imbalance of the gut microbiota and enriched beneficial microbiota, including Akkermansia and Prevotella. The TBF also selectively increased short-chain fatty acid-producing bacteria, including Roseburia and Odoribacter, and decreased the abundance of the diabetes-related gut microbiota, including Escherichia, Mucispirillum, and Bilophila. The correlation analysis indicated that TBFs improved metabolic parameters related to key communities of the gut microbiota. Our data suggested that TBFs alleviated glucose and lipid disturbances and improved colon lesions in diabetic mice, possibly by regulating the community composition of the gut microbiota. This regulation of the gut microbiota composition may explain the observed effects of TBFs to alleviate diabetes-related symptoms.
Keywords: Tartary buckwheat, flavonoids, microbiota, mice
Published in DiRROS: 17.07.2024; Views: 2; Downloads: 2
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16. Biological and genetic characterization of Physostegia chlorotic mottle virus in Europe based on host range, location, and timeColine Temple, Arnaud G. Blouin, Kris De Jonghe, Yoika Foucart, Marleen Botermans, Marcel Westenberg, Ruben Schoen, Pascal Gentit, Michèle Visage, Eric Verdin, Mark Paul Selda Rivarez, Denis Kutnjak, Ana Vučurović, 2022, original scientific article Abstract: Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.
Published in DiRROS: 17.07.2024; Views: 2; Downloads: 0
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17. Natural analogues in pH variability and predictability across the coastal pacific estuaries : extrapolation of the increased oyster dissolution under increased ph amplitude and low predictability related to ocean acidificationNina Bednaršek, Marcus W. Beck, Greg Pelletier, Scott Lee Applebaum, Richard Alan Feely, Robert Butler, Maria Byrne, Betsy Peabody, Jonathan Davis, Jasna Štrus, 2022, original scientific article Abstract: Coastal-estuarine habitats are rapidly changing due to global climate change, with impacts influenced by the variability of carbonate chemistry conditions. However, our understanding of the responses of ecologically and economically important calcifiers to pH variability and temporal variation is limited, particularly with respect to shell-building processes. We investigated the mechanisms driving biomineralogical and physiological responses in juveniles of introduced (Pacific; Crassostrea gigas) and native (Olympia; Ostrea lurida) oysters under flow-through experimental conditions over a six-week period that simulate current and future conditions: static control and low pH (8.0 and 7.7); low pH with fluctuating (24-h) amplitude (7.7 ± 0.2 and 7.7 ± 0.5); and high-frequency (12-h) fluctuating (8.0 ± 0.2) treatment. The oysters showed physiological tolerance in vital processes, including calcification, respiration, clearance, and survival. However, shell dissolution significantly increased with larger amplitudes of pH variability compared to static pH conditions, attributable to the longer cumulative exposure to lower pH conditions, with the dissolution threshold of pH 7.7 with 0.2 amplitude. Moreover, the high-frequency treatment triggered significantly greater dissolution, likely because of the oyster’s inability to respond to the unpredictable frequency of variations. The experimental findings were extrapolated to provide context for conditions existing in several Pacific coastal estuaries, with time series analyses demonstrating unique signatures of pH predictability and variability in these habitats, indicating potentially benefiting effects on fitness in these habitats. These implications are crucial for evaluating the suitability of coastal habitats for aquaculture, adaptation, and carbon dioxide removal strategies.
Keywords: ocean acidification, diel pH variability, amplitude, shell dissolution, predictability
Published in DiRROS: 17.07.2024; Views: 4; Downloads: 2
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18. Pelagic calcifiers face increased mortality and habitat loss with warming and ocean acidificationNina Bednaršek, Brendan Carter, Ryan M. McCabe, Richard Alan Feely, Evan M. Howard, Francisco P. Chavez, Meredith Elliott, Jennifer L. Fisher, Jaime Jahncke, Zach Siegrist, 2022, original scientific article Abstract: Global change is impacting the oceans in an unprecedented way, and multiple lines of evidence suggest that species distributions are changing in space and time. There is increasing evidence that multiple environmental stressors act together to constrain species habitat more than expected from warming alone. Here, we conducted a comprehensive study of how temperature and aragonite saturation state act together to limit Limacina helicina, globally distributed pteropods that are ecologically important pelagic calcifiers and an indicator species for ocean change. We co-validated three different approaches to evaluate the impact of ocean warming and acidification (OWA) on the survival and distribution of this species in the California Current Ecosystem. First, we used colocated physical, chemical, and biological data from three large-scale west coast cruises and regional time series; second, we conducted multifactorial experimental incubations to evaluate how OWA impacts pteropod survival; and third, we validated the relationships we found against global distributions of pteropods and carbonate chemistry. OWA experimental work revealed mortality increases under OWA, while regional habitat suitability indices and global distributions of L. helicina suggest that a multi-stressor framework is essential for understanding pteropod distributions. In California Current Ecosystem habitats, where pteropods are living close to their thermal maximum already, additional warming and acidification through unabated fossil fuel emissions (RCP 8.5) are expected to dramatically reduce habitat suitability.
Keywords: California current ecosystem, climate change, global data synthesis, habitat loss, habitat suitability modeling, multiple stressors, ocean acidification, pelagic calcifiers, pteropods, species distribution, warming
Published in DiRROS: 17.07.2024; Views: 3; Downloads: 3
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19. Benthic-pelagic coupling of marine primary producers under different natural and human-induced pressures’ regimesVasilis Gerakaris, Ioanna Varkitzi, Martina Orlando-Bonaca, Katerina Kikaki, Patricija Mozetič, Polytimi-Ioli Lardi, Konstantinos Tsiamis, Janja Francé, 2022, original scientific article Abstract: Marine primary producers are highly sensitive to environmental deterioration caused by natural and human-induced stressors. Following the Water Framework Directive and the Marine Strategy Framework Directive requirements, the importance of using the different primary producers of the coastal marine ecosystem (pelagic: phytoplankton and benthic: macroalgae and angiosperms) as appropriate tools for an integrated assessment of the ecological status of the coastal environment has been recognized. However, the processes by which water column characteristics and phytobenthic indicators are linked have not been systematically studied. Based on a large dataset from three Mediterranean sub-basins (Adriatic, Ionian and Aegean Seas) with different trophic conditions, this study aims to explore the coupled responses of benthic and pelagic primary producers to eutrophication pressures on a large scale, focusing on the structural and functional traits of benthic macroalgal and angiosperm communities, and to investigate the key drivers among the different eutrophication-related pelagic indicators (such as nutrient and Chl-a concentrations, water transparency, etc.) that can force the benthic system indicators to low ecological quality levels. In addition to the effects of high nutrient loading on phytoplankton biomass, our results also show that increased nutrient concentrations in seawater have a similar effect on macroalgal communities. Indeed, increasing nutrient concentrations lead to increased coverage of opportunistic macroalgal species at the expense of canopy-forming species. Most structural traits of Posidonia oceanica (expressed either as individual metrics: shoot density, lower limit depth and lower limit type, or in the context of PREI index) show opposite trends to increasing levels of pressure indicators such as ammonium, nitrate, phosphate, Chl-a and light attenuation. Furthermore, our results highlight the regulating effect of light availability on the ecological status of seagrass meadows (Posidonia oceanica and Cymodocea nodosa). Increasing leaf length values of C. nodosa are closely associated with higher turbidity values linked to higher phytoplankton biomass (expressed as Chl-a). Overall, the coupling of pelagic and benthic primary producers showed consistent patterns across trophic gradients at the subregional scale.
Keywords: macroalgae, seagrasses, phytoplankton, eutrophication, Mediterranean Sea
Published in DiRROS: 17.07.2024; Views: 4; Downloads: 2
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20. Do cytotoxicity and cell death cause false positive results in the in vitro comet assay?Amaya Azqueta, Helga Stopper, Bojana Žegura, Maria Dusinska, Peter Møller, 2022, original scientific article Abstract: The comet assay is used to measure DNA damage induced by chemical and physical agents. High concentrations of test agents may cause cytotoxicity or cell death, which may give rise to false positive results in the comet assay. Systematic studies on genotoxins and cytotoxins (i.e. non-genotoxic poisons) have attempted to establish a threshold of cytotoxicity or cell death by which DNA damage results measured by the comet assay could be regarded as a false positive result. Thresholds of cytotoxicity/cell death range from 20% to 50% in various publications. Curiously, a survey of the latest literature on comet assay results from cell culture studies suggests that one-third of publications did not assess cytotoxicity or cell death. We recommend that it should be mandatory to include results from at least one type of assay on cytotoxicity, cell death or cell proliferation in publications on comet assay results. A combination of cytotoxicity (or cell death) and proliferation (or colony forming efficiency assay) is preferable in actively proliferating cells because it covers more mechanisms of action. Applying a general threshold of cytotoxicity/cell death to all types of agents may not be applicable; however, 25% compared to the concurrent negative control seems to be a good starting value to avoid false positive comet assay results. Further research is needed to establish a threshold value to distinguish between true and potentially false positive genotoxic effects detected by the comet assay.
Keywords: comet assay, cytotoxicity, genotoxicity, DNA damage, cell death
Published in DiRROS: 17.07.2024; Views: 3; Downloads: 3
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