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- Rohwedder, A., et al.
(author)
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Cloudbuster: a Python-based open source application for three-dimensional reconstruction and quantification of stacked biological imaging samples
- 2022
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In: Interface Focus. - : ROYAL SOC. - 2042-8898 .- 2042-8901. ; 12:5
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Journal article (peer-reviewed)abstract
- Three-dimensional (3D) spheroid cultures are generating increasing interest in cancer research, e.g. for the evaluation of pharmacological effects of novel small molecule inhibitors. This is mainly due to the fact that such 3D structures reflect physiological characteristics of tumours and the cellular microenvironments they reside in more faithfully than two-dimensional (2D) cell cultures; in addition, they allow the reduction of animal experiments while providing significantly relevant human-based models. Quantification of such organoid structures as well as the mainly slice-based acquisition and thus forced 2D representation of 3D spheroids provide a challenge for the interpretation of the associated generated data. Here, we provide a novel open-source workflow to reconstruct a 3D entity from slice-recorded microscopical images with or without treatment with anti-migratory small molecule inhibitors. This reconstruction produces distinct point clouds as basis for subsequent comparison of basic readout parameters using average computer processor, memory and graphics resources within an acceptable time frame. We were able to validate the usefulness of this workflow using 3D data generated by various imaging techniques, including z-stacks from confocal microscopy and histochemically labelled spheroid sectioning, and demonstrate the possibility to accurately characterize inhibitor effects in great detail.
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- Milotić, Tanja, et al.
(author)
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Dung beetle assemblages, dung removal and secondary seed dispersal : data from a large-scale, multi-site experiment in the Western Palaearctic
- 2018
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In: Frontiers of Biogeography. - : eScholarship. - 1948-6596. ; 10:1-2
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Journal article (peer-reviewed)abstract
- By manipulating faeces during feeding and breeding, dung beetles (Coleoptera: Scarabaeidae) fulfil important ecosystem functions in terrestrial ecosystems throughout the world. In a pan-European multi-site experiment (MSE), we estimated the ecosystem functions of dung removal and secondary seed dispersal by differing combinations of dung beetle functional groups. Therefore, we classified dung beetles into five functional groups according to their body size and dung manipulation method: dwellers, large and small tunnelers, and large and small rollers. Furthermore, we set up a dung beetle sampling database containing all sampled dung beetles during the project. By identifying dung beetle specimens to the species level, we obtained a detailed insight into the dung beetle communities at each study location. By establishing experimental plots allowing and inhibiting specific combinations of functional groups in the local dung beetle assemblage from removing dung and seeds, we estimated the role of each group in dung removal and secondary seed dispersal during a 4-week period. We performed all experiments in grazed (semi-) natural grasslands, and used different dung types (cattle, horse, sheep, goat or red deer) to match the herbivore species grazing in close vicinity of each of the study areas. Simultaneously, we sampled dung beetle assemblages by using pitfalls baited with the same dung types as used in the experiments. This data paper documents two datasets collected in the framework of this MSE project. All the experiments took place between 2013 and 2016 at 17 study sites in 10 countries and 11 biogeographic zones. The entire dung beetle sampling dataset was published as a sampling event dataset at GBIF. The dataset includes the sampling results of all 17 study sites, which contain 1,050 sampling events and 4,362 occurrence records of 94 species. The second dataset contains the results of the dung removal and secondary seed dispersal experiments in which we used 11 experimental treatments and the five dung types mentioned above. This experimental results dataset holds all experimental results of the MSE project (11,537 records), and was published in the online data repository Zenodo.
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- Milotic, Tanja, et al.
(author)
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Functionally richer communities improve ecosystem functioning : dung removal and secondary seed dispersal by dung beetles in the Western Palaearctic
- 2019
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In: Journal of Biogeography. - : John Wiley & Sons. - 0305-0270 .- 1365-2699. ; 46:1, s. 70-82
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Journal article (peer-reviewed)abstract
- Aim: In several ecosystems, the diversity of functional species traits has been shown to have a stronger effect on ecosystem functioning than taxonomic diversity alone. However, few studies have explored this idea at a large geographical scale. In a multisite experiment, we unravelled the relationship between ecosystem function and functional completeness of species assemblages using dung beetles as a model group, focusing on dung removal and secondary seed dispersal.Location: Seventeen grassland locations across the Western Palaearctic.Methods: We used a randomized block design with different exclosure types to control the dung and seed removing activities of individual functional groups of the local dung beetle assemblage. We classified dung beetle species according to resource specialization and into functional groups based on dung processing behaviour (dwellers, tunnellers, rollers) and body size (small, large). Additionally, we assessed the role of other soil macro-invertebrates. By sampling the dung beetle community and measuring the remaining dung and seeds after the experiment, the impact of each functional group was estimated.Results: Dung beetle assemblages differed along a north-south and east-west gradient. Dwellers dominated northernmost sites, whereas at lower latitudes we observed more tunnellers and rollers indicating a functional shift. Resource specialists were more abundant in southern and eastern areas. Overall, functional group diversity enhanced dung removal. More dung (+46.9%) and seeds (+32.1%) were removed in the southern sites and tunnellers and rollers were more effective. At the northernmost sites, where tunnellers were scarce or absent, other soil macro-invertebrates removed the majority of dung.Main conclusions: The conservation of functionally complete dung beetle assemblages is crucial to maintain the ecosystem functions provided by dung beetles. Given the latitudinal variation in functional group diversity, it is reasonable to expect compositional changes due to climate change. These changes could lead to increased dung removal and a higher secondary seed dispersal rate in northern regions.
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