611. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potatoTjaša Lukan, Maruša Pompe Novak, Špela Baebler, Magda Tušek-Žnidarič, Aleš Kladnik, Maja Križnik, Andrej Blejec, Maja Zagorščak, Katja Stare, Barbara Dušak, Anna Coll Rius, Stephan Pollmann, Karolina Morgiewicz, Jacek Hennig, Kristina Gruden, 2020, original scientific article Abstract: Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA-seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling. Keywords: immune signaling network, NADPH oxidase RBOHD, reactive oxygen species, salicylic acid, Sola-num tuberosum (potato), spatiotemporal response analysis, virus resistance, Potyvirus Published in DiRROS: 22.07.2024; Views: 148; Downloads: 121
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612. Machine learning approaches identify male body size as the most accurate predictor of species richnessKlemen Čandek, Urška Pristovšek, Matjaž Kuntner, 2020, original scientific article Abstract: Background
A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness –the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera.
Results
We test the predictive power of 22 variables from spiders’ morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness.
Conclusions
We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly. Keywords: biodiversity, lineage diversity, species traits, spiders, phylogenetic diversity, species distribution, random forest, multiple correspondence analysis Published in DiRROS: 22.07.2024; Views: 271; Downloads: 249
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613. Lagrangian modelling of a person lost at sea during the Adriatic scirocco storm of 29 October 2018Matjaž Ličer, Solène Estival, Catalina Reyes-Suarez, Davide Deponte, Anja Fettich, 2020, original scientific article Abstract: On 29 October 2018 a windsurfer's mast broke about 1 km offshore from Istria during a severe scirocco storm in the northern Adriatic Sea. He drifted in severe marine conditions until he eventually beached alive and well in Sistiana (Italy) 24 h later. We conducted an interview with the survivor to reconstruct his trajectory and to gain insight into his swimming and paddling strategy. Part of survivor's trajectory was verified using high-frequency radar surface current observations as inputs for Lagrangian temporal back-propagation from the beaching site. Back-propagation simulations were found to be largely consistent with the survivor's reconstruction. We then attempted a Lagrangian forward-propagation simulation of his trajectory by performing a leeway simulation using the OpenDrift tracking code using two object types: (i) person in water in unknown state and (ii) person with a surfboard. In both cases a high-resolution (1 km) setup of the NEMO v3.6 circulation model was employed for the surface current component, and a 4.4 km operational setup of the ALADIN atmospheric model was used for wind forcing. The best performance is obtained using the person-with-a-surfboard object type, giving the highest percentage of particles stranded within 5 km of the beaching site. Accumulation of particles stranded within 5 km of the beaching site saturates 6 h after the actual beaching time for all drifting-particle types. This time lag most likely occurs due to poor NEMO model representation of surface currents, especially in the final hours of the drift. A control run of wind-only forcing shows the poorest performance of all simulations. This indicates the importance of topographically constrained ocean currents in semi-enclosed basins even in seemingly wind-dominated situations for determining the trajectory of a person lost at sea. Published in DiRROS: 22.07.2024; Views: 146; Downloads: 95
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614. 2D and 3D in vitro assays to quantify the invasive behavior of glioblastoma stem cells in response to SDF-1[alpha]Vashendriya V. V. Hira, Barbara Breznik, Cornelis J. F. van Noorden, Tamara Lah Turnšek, Remco J. Molenaar, 2020, original scientific article Abstract: Invasion is a hallmark of cancer and therefore in vitro invasion assays are important tools in cancer research. We aimed to describe in vitro 2D transwell assays and 3D spheroid assays to quantitatively determine the invasive behavior of glioblastoma stem cells in response to the chemoattractant SDF-1α. Matrigel was used as a matrix in both assays. We demonstrated quantitatively that SDF-1α increased invasive behavior of glioblastoma stem cells in both assays. We conclude that the 2D transwell invasion assay is easy to perform, fast and less complex whereas the more time-consuming 3D spheroid invasion assay is physiologically closer to the in vivo situation. Keywords: 2D transwell invasion assay, 3D spheroid invasion assay, cancer cell, cellular invasion, glioblastoma stem cells Published in DiRROS: 22.07.2024; Views: 138; Downloads: 130
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615. The effect of three polyphenols and some other anti-oxidant substances on amyloid fibril formation by human cystatin CAlma Jahić, Magda Tušek-Žnidarič, Sara Pintar, Selma Berbić, Eva Žerovnik, 2020, original scientific article Abstract: Human cystatin C (CysC) is an amyloid forming protein involved in the hereditary cerebral amyloid angiopathy (HCCAA) that affects arteries in the brain and the peripheral nervous system. In this study we measured the influence of several substances on human CysC aggregation and amyloid fibril formation, induced at pH 4 in vitro. The effect of three polyphenols: resveratrol, quercetin and curcumin and of two antioxidants: vitamin C (VitC) and N-acetyl-L-cysteine (NAC) was explored as well as the effect of sulphoraphane (SF) and α-lipoic acid (AL). The formation of amyloid fibrils was followed by Thioflavin T (ThT) fluorescence and by transmission electron microscopy (TEM). Effects on the length of the lag phase were revealed by following the increase of ThT fluorescence intensity with time. The amount and morphology of fibrils in comparison to prefibrillar aggregates and globular oligomers were evaluated by TEM at the plateau stage of the reaction. Thermal stabilization of the CysC monomer by the small compounds was measured by differential scanning fluorimetry (DSF). NAC, VitC and SF exhibited the largest inhibitory effect on amyloid fibril growth. The effects of polyphenols were not significant, apart from resveratrol, which partly inhibited the amyloid fibril growth. Published in DiRROS: 22.07.2024; Views: 132; Downloads: 86
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616. Validating the potential of double-stranded RNA targeting Colorado potato beetle mesh gene in laboratory and field trialsMarko Petek, Anna Coll Rius, Rok Ferenc, Jaka Razinger, Kristina Gruden, 2020, original scientific article Abstract: Colorado potato beetle (CPB) is an agricultural pest of solanaceous crops, notorious for its rapid resistance development to chemical pesticides. Foliar spraying of dsRNA formulations is a promising innovative technology providing highly specific and environmentally acceptable option for CPB management. We designed dsRNA to silence CPB mesh gene (dsMESH) and performed laboratory feeding trials to assess impacts on beetle survival and development. We compared the effectiveness of in vivo and in vitro produced dsRNA in a series of laboratory experiments. We additionally performed a field trial in which the efficacy of dsRNA sprayed onto potato foliage was compared to a spinosad-based insecticide. We showed that dsMESH ingestion consistently and significantly impaired larval growth and decreased larval survival in laboratory feeding experiments. In vivo produced dsRNA performed similarly as in vitro synthesized dsRNA in laboratory settings. In the field trial, dsMESH was as effective in controlling CPB larvae as a commercial spinosad insecticide, its activity was however slower. We discuss limitations and benefits of a potential dsMESH-based CPB management strategy and list some important RNAi based CPB research topics, which will have to be addressed in future. Keywords: RNA interference, RNA interference feeding, ds RNA, gene silencing, RNAi pest control, survival analysis, field trial Published in DiRROS: 22.07.2024; Views: 145; Downloads: 54
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617. Development and validation of a new TaqMan real-time PCR for detection of 'Candidatus phytoplasma pruni'Zala Kogej Zwitter, Marina Dermastia, Nataša Mehle, 2020, original scientific article Abstract: Phytoplasmas of the 16SrIII group are wide spread, and have a broad plant host range. Among these, ‘Candidatus phytoplasma pruni’ (‘Ca. P. pruni’; phytoplasmas of 16SrIII subgroup A) can cause serious diseases in Prunus species and ‘Ca. P. pruni’-related strains can infect other plant species, including grapevines. In this study, a new real-time PCR detection system was developed for ‘Ca. P. pruni’ using TaqMan chemistry. This test was designed to detect ‘Ca. P. pruni’, by amplifying the species-specific secY gene. In addition, a test to amplify the group-specific 16S rRNA gene region was also developed. The performances of both tests were evaluated. The test that amplifies the secY gene provided reliable and quick detection of ‘Ca. P. pruni’. Using the newly developed and validated test, ‘Ca. P. pruni’ was not found in any of the 434 field samples collected from different plants species grown in different regions of Slovenia. Keywords: phytoplasma, X-disease, real-time PCR, Prunus Published in DiRROS: 22.07.2024; Views: 148; Downloads: 150
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618. The depleted carbon isotopic signature of nematodes and harpacticoids and their place in carbon processing in fish farm sedimentsMateja Grego, Alenka Malej, Marleen De Troch, 2020, original scientific article Abstract: Fish farm-originating organic matter can modify the ecological processes in a benthic ecosystem. This was investigated in the sediments of the northern Adriatic Sea by measuring δ13C signature of nematodes, harpacticoids, and sedimentary organic matter, and by assessing pore water nutrients and bacterial composition. In a mesocosm experiment, 13C-labeled diatoms were added on top of sediment cores and 13C enrichment was measured as a proxy of diatom uptake by meiofauna. The δ13C signatures were depleted under fish farming cages compared to the reference site, as observed for sedimentary organic matter (−24.4‰ vs. −21.8‰), for nematodes (−22.5‰ vs. −17.7‰), and for harpacticoids (−25.3‰ vs. −20.8‰). The direct consumption of fish feed (−22.2‰) was not traced in meiofauna taxa. Nematodes from the farm site likely reflect a diet comprising sedimentary organic matter, as they were enriched by 2‰ relative to the sedimentary organic matter. The nematodes from the reference site were enriched by 4.2‰ relative to the sedimentary organic matter, which implies that they rely on more enriched food sources, like diatoms, which was confirmed by their uptake of 13C-labeled diatoms. The nematode assemblage incorporated more diatom 13C than harpacticoids, making them more important players in the carbon flux from diatoms to higher trophic levels at the reference site. Harpacticoids from the reference site were enriched by 1.1‰ compared to sedimentary organic matter, implying that this was their primary food source. Harpacticoids from the farm site were depleted by 0.9‰ relative to the sedimentary organic matter, indicating they were influenced by a very depleted food source like bacteria. Harpacticoids from both the cage and reference sites consumed 13C-labeled diatoms, which implies their diet might span a broad δ13C range, from bacteria to diatoms. Pore water nutrients with high dissolved inorganic carbon, phosphate, and ammonium concentration indicated an elevated microbial degradation of organic compounds under the fish farm. The denaturing gradient gel electrophoresis analysis showed a 70% similarity between sediment bacteria communities from the fish farm and reference site. The study demonstrated that fish farm-originating organic matter enters the meiofauna food chain, and that nematodes and harpacticoids use different food sources under the fish farm and at the reference site. Published in DiRROS: 22.07.2024; Views: 123; Downloads: 104
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619. Supporting dataset and methods for body sizes and concentrations of chemical elements measured in elytra and abdomens of Stag Beetles Lucanus cervusGrzegorz Orłowski, Lucyna Mróz, Marcin Kadej, Adrian Smolis, Dariusz Tarnawski, Jerzy Karg, Alessandro Campanaro, Marco Bardiani, Deborah J. Harvey, Marcos Méndez, Arno Thomaes, Al Vrezec, Krzysztof Ziomek, Andrzej L. Rudecki, Detlef Mader, 2020, original scientific article Abstract: The dataset presented in this data paper supports “Breaking down insect stoichiometry into chitin-based and internal elemental traits: Patterns and correlates of continent-wide intraspecific variation in the largest European saproxylic beetle” (Orłowski et al. 2020). Here we present the supplementary data and description of methods on the following: (1) mass of elytra and abdomens across 28 local Stag Beetle Lucanus cervus populations in Europe. (2) Population origin and coverage of six major land-cover types, including transport infrastructure, measured in three radii (500 m, 1000 m and 5000 m) around the sampling sites of these populations. (3) The relationship between the mass and concentrations of elements measured in abdomens and elytra in 28 Stag Beetle populations and major land-cover types around the sampling sites. Keywords: elemental composition, trace elements, internal metal concentrations, exoskeleton, chitin-bound metals Published in DiRROS: 22.07.2024; Views: 126; Downloads: 83
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620. Evidence for senescence in survival but not in reproduction in a short-lived passerineRémi Fay, Michael Schaub, Jennifer A. Border, Ian G. Henderson, Georg Fahl, Jürgen Feulner, Petra Horch, Mathis Müller, Helmut Rebstock, Dmitry Shitikov, Davorin Tome, Matthias Vögeli, Martin U. Grüebler, 2020, original scientific article Abstract: Senescence has been studied since a long time by theoreticians in ecology and evolution, but empirical support in natural population has only recently been accumulating. One of the current challenges is the investigation of senescence of multiple fitness components and the study of differences between sexes. Until now, studies have been more frequently conducted on females than on males and rather in long-lived than in short-lived species. To reach a more fundamental understanding of the evolution of senescence, it is critical to investigate age-specific survival and reproduction performance in both sexes and in a large range of species with contrasting life histories. In this study, we present results on patterns of age-specific and sex-specific variation in survival and reproduction in the whinchat Saxicola rubetra, a short-lived passerine. We compiled individual-based long-term datasets from seven populations that were jointly analyzed within a Bayesian modeling framework. We found evidence for senescence in survival with a continuous decline after the age of 1 year, but no evidence of reproductive senescence. Furthermore, we found no clear evidence for sex effects on these patterns. We discuss these results in light of previous studies documenting senescence in short-lived birds. We note that most of them have been conducted in populations breeding in nest boxes, and we question the potential effect of the nest boxes on the shape of age-reproductive trajectories. Keywords: actuarial senescence, age-specific demographic rate, aging, Saxicola rubetra, whinchat Published in DiRROS: 22.07.2024; Views: 134; Downloads: 85
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