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1.
GoMapMan : integration, consolidation and visualization of plant gene annotations within the MapMan ontology
Živa Ramšak, Špela Baebler, Ana Rotter, Matej Korbar, Igor Mozetič, Björn Usadel, Kristina Gruden, 2014, original scientific article

Abstract: GoMapMan (http://www.gomapman.org) is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis and three crop species (potato, tomato and rice) are included. The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.
Keywords: genes, plants
Published in DiRROS: 02.08.2024; Views: 93; Downloads: 71
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2.
Host range and symptomatology of Pepino mosaic virus strains occurring in Europe
Dag-Ragnar Blystad, René van der Vlugt, Ana Alfaro-Fernández, María del Carmen Córdoba, Gábor Bese, Dimitrinka Hristova, Henryk Pospieszny, Nataša Mehle, Maja Ravnikar, Laura Tomassoli, Christina Varveri, Steen Lykke Nielsen, 2015, original scientific article

Abstract: Pepino mosaic virus (PepMV) has caused great concern in the greenhouse tomato industry after it was found causing a new disease in tomato in 1999. The objective of this paper is to investigate alternative hosts and compare important biological characteristics of the three PepMV strains occurring in Europe when tested under different environmental conditions. To this end we compared the infectivity and symptom development of three, well characterized isolates belonging to three different PepMV strains, EU-tom, Ch2 and US1, by inoculating them on tomato, possible alternative host plants in the family Solanaceae and selected test plants. The inoculation experiments were done in 10 countries from south to north in Europe. The importance of alternative hosts among the solanaceous crops and the usefulness of test plants in the biological characterization of PepMV isolates are discussed. Our data for the three strains tested at 10 different European locations with both international and local cultivars showed that eggplant is an alternative host of PepMV. Sweet pepper is not an important host of PepMV, but potato can be infected when the right isolate is matched with a specific cultivar. Nicotiana occidentalis 37B is a useful indicator plant for PepMV studies, since it reacts with a different symptomatology to each one of the PepMV strains.
Keywords: Pepino mosaic virus, potexvirus, strains, host plants, test plants
Published in DiRROS: 26.07.2024; Views: 104; Downloads: 121
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3.
Novel, male-produced aggregation pheromone of the cerambycid beetle Rosalia alpina, a priority species of European conservation concern
Alenka Žunič Kosi, Yunfan Zou, Michal Hoskovec, Al Vrezec, Nataša Stritih Peljhan, Jocelyn G. Millar, 2017, original scientific article

Abstract: Several recent studies have demonstrated the great potential for exploiting semiochemicals in ecology and conservation studies. The cerambycid beetle Rosalia alpina represents one of the flagship species of saproxylic insect biodiversity in Europe. In recent years its populations appear to have declined substantially, and its range has shrunk considerably as a result of forest management and urbanization. Here, we collected volatile chemicals released by males and females of R. alpina. Analyses of the resulting extracts revealed the presence of a single male-specific compound, identified as a novel alkylated pyrone structure. In field bioassays in Slovenia, traps baited with the synthesized pyrone captured both sexes of R. alpina, indicating that the pyrone functions as an aggregation pheromone. Our results represent the first example of a new structural class of pheromones within the Cerambycidae, and demonstrate that pheromone-baited traps can provide a useful tool for sampling R. alpina. This tool could be particularly useful in the ongoing development of conservation strategies for the iconic but endangered Alpine longicorn.
Keywords: pheromones, beetles, plants, endangered species, conservation science
Published in DiRROS: 25.07.2024; Views: 114; Downloads: 259
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4.
Arsenic in sediments, soil and plants in a remediated area of the Iron Quadrangle, Brazil, and its accumulation and biotransformation in Eleocharis geniculata
Maria-Angela Menezes, Ingrid Falnoga, Zdenka Šlejkovec, Radojko Jaćimović, Nilton Couto, Eleonora Deschamps, Jadran Faganeli, 2020, original scientific article

Abstract: Since arsenic (As) exposure is largely due to geochemical contamination, this study focused on the remediated area of Santana do Morro, a district of Santa Bárbara, Minas Gerais, Brazil, which was previously contaminated with As due to gold mining. Total As concentrations in sediment, soil and plants were determined, next to As species, anionic arsenic compounds As(III), As(V), monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA), in plants samples. Total As concentrations in soil and sediments were slightly elevated (16-18 µg g-1) and most of the plants contained low levels of As (< 1 µg g-1). The exception was a native plant Eleocharis geniculata (L.) which contained elevated levels of As (4 µg g-1). The exposure of this plant to As under controlled conditions (hydroponics) indicated its possible tolerance to elevated As levels and suggesting its potential use in phytomonitoring of As-contaminated sites. This plant is able to metabolize arsenate to arsenite and contained MMA and DMA, both in its natural habitat and under controlled conditions.
Keywords: arsenic species, soil, sediments, plants, Cyperacea, Iron Quadrangle
Published in DiRROS: 22.07.2024; Views: 123; Downloads: 64
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5.
ReSurveyEurope : a database of resurveyed vegetation plots in Europe
Ilona Knollová, Milan Chytrý, Helge Bruelheide, Stefan Dullinger, Ute Jandt, Markus Bernhardt-Römermann, Idoia Biurrun, Francesco de Bello, Michael Glaser, Stephan M. Hennekens, Mateja Germ, Aleksandra Golob, Janez Kermavnar, Lado Kutnar, Urban Šilc, 2024, review article

Abstract: Aims We introduce ReSurveyEurope — a new data source of resurveyed vegetation plots in Europe, compiled by a collaborative network of vegetation scientists. We describe the scope of this initiative, provide an overview of currently available data, governance, data contribution rules, and accessibility. In addition, we outline further steps, including potential research questions. Results ReSurveyEurope includes resurveyed vegetation plots from all habitats. Version 1.0 of ReSurveyEurope contains 283,135 observations (i.e., individual surveys of each plot) from 79,190 plots sampled in 449 independent resurvey projects. Of these, 62,139 (78%) are permanent plots, that is, marked in situ, or located with GPS, which allow for high spatial accuracy in resurvey. The remaining 17,051 (22%) plots are from studies in which plots from the initial survey could not be exactly relocated. Four data sets, which together account for 28,470 (36%) plots, provide only presence/absence information on plant species, while the remaining 50,720 (64%) plots contain abundance information (e.g., percentage cover or cover–abundance classes such as variants of the Braun-Blanquet scale). The oldest plots were sampled in 1911 in the Swiss Alps, while most plots were sampled between 1950 and 2020. Conclusions ReSurveyEurope is a new resource to address a wide range of research questions on fine-scale changes in European vegetation. The initiative is devoted to an inclusive and transparent governance and data usage approach, based on slightly adapted rules of the well-established European Vegetation Archive (EVA). ReSurveyEurope data are ready for use, and proposals for analyses of the data set can be submitted at any time to the coordinators. Still, further data contributions are highly welcome.
Keywords: biodiversity, monitoring, species richness, vascular plants, vegetation dynamics
Published in DiRROS: 23.04.2024; Views: 323; Downloads: 138
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6.
Habitat degradation facilitates the invasion of Neophytes : a resurvey study based on permanent vegetation plots in oak forests in Slovenia (Europe)
Janez Kermavnar, Lado Kutnar, 2024, original scientific article

Abstract: The spread of neophytes (non-native plant species) challenges the conservation status and ecological integrity of forests, especially in lowland areas. Long-term resurvey studies are needed to evaluate the temporal dynamics of neophytes in forests; however, such data are scarce. In 2023, we resampled a set of 45 permanent vegetation plots (established in 1992/93) in two forest vegetation types: oak–hornbeam forests dominated by Quercus robur and colline oak–beech forests dominated by Q. petraea. Over the last 30 years, oak forests have experienced extensive oak tree mortality, with the degree of habitat degradation being greater in Q. robur forests. In the early 1990s, only three neophytes with low abundance were recorded across all plots. In the 2023 resurvey, the total number of neophytes increased to 22 species (15 herbaceous and 7 woody species), comprising 6.9% of the total species pool in the understory layer. The increase in the plot-level number and cover of neophytes was significant in plots dominated by Q. robur but not in those with Q. petraea. The most frequent neophytes were Impatiens parviflora (present in 31% of plots), Solidago gigantea (27%), Erigeron annuus (16%) and Erechtites hieraciifolia (16%). The richness and cover of neophytes were significantly affected by the tree layer cover (negative correlation) and the degree of soil disturbance (positive correlation). All neophytes established in disturbed patches, whereas the occurrence of I. parviflora was exceptional as it was able to colonize less degraded, shaded understory environments. Habitat degradation (the mortality-induced loss of stand-forming oak trees resulting in extensive tree layer cover decrease) emerged as a key driver promoting neophyte proliferation, coupled with the impact of management-induced disturbances affecting overstory and soil conditions. The spread is expected to continue or even intensify in the future because novel light regimes and disturbances make forest habitats less resistant to neophyte proliferation.
Keywords: long-term vegetation change, invasive non-native plants, oak mortality, Quercus robur, Quercus petraea, canopy openness, Impatiens parviflora, Slovenia
Published in DiRROS: 19.04.2024; Views: 288; Downloads: 141
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7.
Contrasting responses of alien and ancient forest indicator plant species to fragmentation process in the temperate lowland forests
Mirjana Šipek, Lado Kutnar, Aleksander Marinšek, Nina Šajna, 2022, original scientific article

Abstract: Fragmentation is one of the major threats to biodiversity. In a fragmented landscape, forest specialists are losing suitable forest habitats with specific site and microclimate conditions, which results in their local extinction. Conversely, the invasion of alien species is facilitated by open forest areas and increased boundaries between forest fragments and adjacent land. We studied the effect of fragmentation in terms of fragment size impact on overall plant species richness and on selected ecologically important groups' richness, composition, and diversity. We surveyed vegetation in the interior of 47 fragments of various sizes and one unfragmented reference forest. Our results reveal that the effect of fragmentation is complex and differs for studied plant groups. Decreasing fragment size negatively affects the overall plant richness and richness of native and ancient forest indicator plants as well as their diversity, while the effect is positive for alien plants. The highest proportion of ancient forest indicator plant species and the lowest proportion of alien plants in the unfragmented forest underline the great conservation value of forest fragments. At the same time, our results reveal that large and diverse forest ecosystems are susceptible to biological invasions as well.
Keywords: forest fragment, indicator plants, invasion, diversity, habitat modification, habitat conservation
Published in DiRROS: 15.05.2023; Views: 503; Downloads: 259
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8.
Are ecological niche optimum and width of forest plant species related to their functional traits?
Janez Kermavnar, Lado Kutnar, Aleksander Marinšek, Valerija Babij, 2023, original scientific article

Abstract: The ecological niche is one of the central concepts in plant ecology. Understanding which biological traits influence plant niches remains limited, preventing large-scale generalizations. Using a representative pool of 94 herb-layer species frequently occurring in the Slovenian forest vegetation types and an extensive suite of 28 plant functional traits, we tested whether traits serve as predictors for the optimum and width of plant species ecological niche. Niche optimum (mean) and niche width (standard deviation) of each species were derived from community-level ecological indicator values for six environmental gradients, i.e., light, temperature, continentality, moisture, soil reaction and nutrients. We investigated relationships between niche parameters and functional traits through a random forest analysis to account for relatively high trait correlations. Our results suggest that niche optimum and width of forest plant species are related to their functional traits. The two niche parameters were best explained by similar set of traits; however, the relative importance of traits differed substantially. Traits associated with disturbances (frequency and severity), plant dispersal (seed mass, dispersal syndrome), leaf economics spectrum (specific leaf area) and life strategy (CSR scores) showed the highest overall significance in predicting niche optimum and width. Functional traits were, on average, better predictors for niche optimum (average variance explained across all six environmental factors: 20.2%) than for niche width (average variance explained: 7.7%). Intraspecific trait variability, not considered in this study, likely plays an important role in case of niche width. The analyses suggest that, while not all traits impact niche parameters to the same degree, it is crucial to consider traits representing different ecological dimensions and revealing leading patterns of trait coordination. We recommend that the relative importance of traits for species niche parameters should be tested on a larger spatial scale using broader pool of forest understory plants across Europe.
Keywords: ecological gradients, Ellenberg indicator values, Slovenian forest types, trait-environment relationship, understory plants
Published in DiRROS: 09.03.2023; Views: 603; Downloads: 371
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9.
Passive shoulder exoskeletons : more effective in the lab than in the field?
Sander De Bock, Jo Ghillebert, Renée Govaerts, Shirley A. Elprama, Uroš Marušič, Ben Serrien, An Jacobs, Joost Geeroms, Romain Meeusen, Kevin De Pauw, 2021, original scientific article

Abstract: Shoulder exoskeletons potentially reduce overuse injuries in industrial settings including overhead work or lifting tasks. Previous studies evaluated these devices primarily in laboratory setting, but evidence of their effectiveness outside the lab is lacking. The present study aimed to evaluate the effectiveness of two passive shoulder exoskeletons and explore the transfer of laboratory-based results to the field. Four industrial workers performed controlled and in-field evaluations without and with two exoskeletons, ShoulderX and Skelex in a randomized order. The exoskeletons decreased upper trapezius activity (up to 46%) and heart rate in isolated tasks. In the field, the effects of both exoskeletons were less prominent (up to 26% upper trapezius activity reduction) while lifting windscreens weighing 13.1 and 17.0 kg. ShoulderX received high discomfort scores in the shoulder region and usability of both exoskeletons was moderate. Overall, both exoskeletons positively affected the isolated tasks, but in the field the support of both exoskeletons was limited. Skelex, which performed worse in the isolated tasks compared to ShoulderX, seemed to provide the most support during the in-field situations. Exoskeleton interface improvements are required to improve comfort and usability. Laboratory-based evaluations of exoskeletons should be interpreted with caution, since the effect of an exoskeleton is task specific and not all infield situations with high-level lifting will equally benefit from the use of an exoskeleton. Before considering passive exoskeleton implementation, we recommend analyzing joint angles in the field, because the support is inherently dependent on these angles, and to perform in-field pilot tests. This paper is the first thorough evaluation of two shoulder exoskeletons in a controlled and infield situation.
Keywords: assistive devices, exoskeletons, ergonomics, industrial plants, system validation
Published in DiRROS: 28.02.2022; Views: 833; Downloads: 608
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10.
Different belowground responses to elevated ozone and soil water deficit in three European oak species (Quercus ilex, Q. pubescens and Q. robur)
Tanja Mrak, Ines Štraus, Tine Grebenc, Jožica Gričar, Yasutomo Hoshika, Giulia Carriero, Elena Paoletti, Hojka Kraigher, 2019, original scientific article

Abstract: Effects on roots due to ozone and/or soil water deficit often occur through diminished belowground allocation of carbon. Responses of root biomass, morphology, anatomy and ectomycorrhizal communities were investigated in seedlings of three oak species: Quercus ilex L., Q. pubescens Willd. and Q. robur L., exposed to combined effects of elevated ozone (ambient air and 1.4 x ambient air) and water deficit (100% and 10% irrigation relative to field capacity) for one growing season at a free-air ozone exposure facility. Effects on root biomass were observed as general reduction in coarse root biomass by -26.8 % and in fine root biomass by -13.1 % due to water deficit. Effect on coarse root biomass was the most prominent in Q. robur (-36.3 %). Root morphological changes manifested as changes in proportions of fine root (<2 mm) diameter classes due to ozone and water deficit in Q. pubescens and due to water deficit in Q. robur. In addition, reduced fine root diameter (-8.49 %) in Q. robur was observed under water deficit. Changes in root anatomy were observed as increased vessel density (+18.5 %) due to ozone in all three species, as reduced vessel tangential diameter (-46.7 %) in Q. ilex due to interaction of ozone and water, and as generally increased bark to secondary xylem ratio (+47.0 %) due to interaction of ozone and water. Water deficit influenced occurrence of distinct growth ring boundaries in roots of Q. ilex and Q. robur. It shifted the ectomycorrhizal community towards dominance of stress-resistant species, with reduced relative abundance of Tomentella sp. 2 and increased relative abundances of Sphaerosporella brunnea and Thelephora sp. Our results provide evidence that expression of stress effects varies between root traits; therefore the combined analysis of root traits is necessary to obtain a complete picture of belowground responses.
Keywords: ozone, drought, fine roots, ectomycorrhiza, anatomy, morphology, plants
Published in DiRROS: 20.02.2020; Views: 2241; Downloads: 1475
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