1331. 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: 395; Downloads: 184
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1332. 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: 270; Downloads: 281
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1333. 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: 284; Downloads: 266
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1334. 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: 308; Downloads: 185
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1335. 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: 302; Downloads: 225
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1336. Synthetic cannabinoid WIN 55,212–2 inhibits growth and induces cell death of oral and pancreatic stem-like/poorly differentiated tumor cellsMeng-Wei Ko, Barbara Breznik, Emanuela Senjor, Anahid Jewett, 2022, original scientific article Abstract: We report here that synthetic cannabinoid WIN 55,212–2 inhibits tumor cell proliferation and induces cell death of oral and pancreatic tumor cells, and the effect is much more pronounced on stem-like/poorly differentiated OSCSCs and MP2 cells when compared to well-differentiated OSCCs, and PL-12 tumor cells. In addition, WIN 55,212-2 decreases cell surface expression of CD44, CD54, MHC class I and PD-L1 on oral and pancreatic tumor cells with the exception of PD-L1 expression on well-differentiated PL-12 pancreatic tumor cells which exhibits an increase in the expression rather than a decrease. Overall, we demonstrate that WIN 55,212-2 has an increased targeting activity against cancer stem cells/poorly differentiated oral and pancreatic tumor cells when compared to well-differentiated tumor cells, and furthermore, such differences in function do not correlate with the levels of CB1 and CB2 receptor expression on tumor cells, suggesting it's function either through post-receptor mediated activation and/or yet-to-be identified novel receptors. Intraperitoneal (IP) delivery of WIN 55-212-2 in humanized BLT mice is found to impart an activating potential for NK cells demonstrating increased NK cell mediated cytotoxicity and secretion of IFN-γ in our preliminary experiments. These results not only suggest a direct targeting of CSCs/poorly differentiated tumors by WIN 55-212-2 but also by indirect targeting of such tumors through the activation and increased functions of NK cells.
Keywords: cancer stem cells, cannabinoids, cell death, cancer biology, genetic toxicology
Published in DiRROS: 17.07.2024; Views: 309; Downloads: 183
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1337. Male mating strategies to counter sexual conflict in spidersShichang Zhang, Long Yu, Min Tan, Noeleen Y. L. Tan, Xaven X. B. Wong, Matjaž Kuntner, Daiqin Li, 2022, original scientific article Abstract: When sexual conflict selects for reproductive strategies that only benefit one of the sexes, evolutionary arms races may ensue. Female sexual cannibalism is an extreme manifestation of sexual conflict. Here we test two male mating strategies aiming at countering sexual cannibalism in spiders. The “better charged palp” hypothesis predicts male selected use of the paired sexual organ (palp) containing more sperm for their first copulation. The “fast sperm transfer” hypothesis predicts accelerated insemination when cannibalism is high. Our comparative tests on five orbweb spider species with varying levels of female sexual cannibalism and sexual size dimorphism (SSD) reveal that males choose the palp with more sperm for the first copulation with cannibalistic females and that males transfer significantly more sperm if females are cannibalistic or when SSD is biased. By supporting the two hypotheses, these results provide credibility for male mating syndrome. They, however, open new questions, namely, how does a male differentiate sperm quantities between his palps? How does he perform palp choice after assessing his cannibalistic partner? By conducting follow-up experiments on Nephilengys malabarensis, we reveal that it is sperm volume detection, rather than left-right palp dominance, that plays prominently in male palp choice.
Keywords: spiders, sexual conflict, female sexual cannibalism
Published in DiRROS: 17.07.2024; Views: 271; Downloads: 212
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1338. Physiological and transcriptional responses to saline irrigation of young ‘Tempranillo’ vines grafted onto different rootstocksIgnacio Buesa, Juan G. Pérez-Pérez, Fernando Visconti, Rebeka Strah, Diego S. Intrigliolo, Luis Bonet, Kristina Gruden, Maruša Pompe Novak, Jose M. de Paz, 2022, original scientific article Abstract: The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young ‘Tempranillo’ (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m–1 and a Saline treatment with 3.5 dS m–1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl– and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards.
Keywords: osmotic adjustment, gas exchange, gene expression, water relations, Vitis vinifera L. (grapevine), salinity tolerance
Published in DiRROS: 17.07.2024; Views: 305; Downloads: 222
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1339. PaintOmics 4 : new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databasesTianyuan Liu, Pedro Salguero, Marko Petek, Carlos Martinez-Mira, Leandro Balzano-Nogueira, Živa Ramšak, Lauren McIntyre, Kristina Gruden, Sonia Tarazona, Ana Conesa, 2022, original scientific article Abstract: PaintOmics is a web server for the integrative analysis and visualisation of multi-omics datasets using biological pathway maps. PaintOmics 4 has several notable updates that improve and extend analyses. Three pathway databases are now supported: KEGG, Reactome and MapMan, providing more comprehensive pathway knowledge for animals and plants. New metabolite analysis methods fill gaps in traditional pathway-based enrichment methods. The metabolite hub analysis selects compounds with a high number of significant genes in their neighbouring network, suggesting regulation by gene expression changes. The metabolite class activity analysis tests the hypothesis that a metabolic class has a higher-than-expected proportion of significant elements, indicating that these compounds are regulated in the experiment. Finally, PaintOmics 4 includes a regulatory omics module to analyse the contribution of trans-regulatory layers (microRNA and transcription factors, RNA-binding proteins) to regulate pathways. We show the performance of PaintOmics 4 on both mouse and plant data to highlight how these new analysis features provide novel insights into regulatory biology.
Keywords: PaintOmics 4, web tools, datasets, analysis methods, molecular biology
Published in DiRROS: 17.07.2024; Views: 287; Downloads: 217
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