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- Culina, Antica, et al.
(författare)
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Connecting the data landscape of long-term ecological studies : The SPI-Birds data hub
- 2021
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Ingår i: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 90:9, s. 2147-2160
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Tidskriftsartikel (refereegranskat)abstract
- The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database ()-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
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| 2. |
- Ellis, Vincenzo A., et al.
(författare)
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Explaining prevalence, diversity and host specificity in a community of avian haemosporidian parasites
- 2020
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Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 129:9, s. 1314-1329
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Tidskriftsartikel (refereegranskat)abstract
- Many hypotheses attempt to explain parasite–host associations, but rarely are they examined together in a single community. For hosts, key traits are the proportion of infected individuals (prevalence) and the diversity of parasites infecting them. A key parasite trait is host specificity, ranging from specialists infecting one or a few closely related species to generalists infecting many species. We tested 10 hypotheses to explain host-parasite associations; five ‘host-centric’ (e.g. prevalence is related to host abundance) and five ‘parasite-centric’ (e.g. parasite abundance is related to host specificity). We analyzed a community of 67 locally transmitted avian haemosporidian parasite lineages (genera Plasmodium, Haemoproteus or Leucocytozoon), sampled from 2726 birds (64 species) in southern Sweden. Among host-centric hypotheses, Haemoproteus and Leucocytozoon prevalence and Haemoproteus diversity were related to host habitat preferences, whereas there were no relationships with host abundance or body mass. Haemoproteus and Leucocytozoon prevalences were more similar among closely related than among distantly related host species. Haemoproteus prevalence and diversity were lower in host species with few close relatives (‘evolutionarily distinct’ hosts). Among parasite-centric hypotheses, most lineages, even relative generalists, infected closely related host species more often than expected by chance. However, the host species of Haemoproteus and Leucocytozoon lineages overlapped less among lineages than expected by chance. Specialists did not reach higher prevalences than generalists on single host species. However, the abundance of Haemoproteus lineages was related to host specificity with generalists more common than specialists; this was driven by three closely related generalists. Host specificity of parasites was unrelated to the abundance or evolutionarily distinctiveness of their hosts. Parasite communities are likely structured by many factors and cannot be explained by hypotheses focusing solely on hosts or parasites. However, we found consistent effects of host phylogenetic relationships, plausibly a result of evolutionarily conserved host immune systems limiting parasite distributions.
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| 4. |
- Lunde, Ngoc Nguyen, et al.
(författare)
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Legumain is upregulated in acute cardiovascular events and associated with improved outcome - potentially related to anti-inflammatory effects on macrophages
- 2020
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Ingår i: Atherosclerosis. - : Elsevier. - 0021-9150 .- 1879-1484. ; 296, s. 74-82
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Tidskriftsartikel (refereegranskat)abstract
- Background and aims: We have previously found increased levels of the cysteine protease legumain in plasma and plaques from patients with carotid atherosclerosis. This study further investigated legumain during acute cardiovascular events.Methods: Circulating levels of legumain from patients and legumain released from platelets were assessed by enzyme-linked-immunosorbent assay. Quantitative PCR and immunoblotting were used to study expression, while localization was visualized by immunohistochemistry.Results: In the SUMMIT Malmo cohort (n = 339 with or without type 2 diabetes and/or cardiovascular disease [CVD], and 64 healthy controls), the levels of circulating legumain were associated with the presence of CVD in non-diabetics, with no relation to outcome. In symptomatic carotid plaques and in samples from both coronary and intracerebral thrombi obtained during acute cardiovascular events, legumain was co-localized with macrophages in the same regions as platelets. In vitro, legumain was shown to be present in and released from platelets upon activation. In addition, THP-1 macrophages exposed to releasate from activated platelets showed increased legumain expression. Interestingly, primary peripheral blood mononuclear cells stimulated with recombinant legumain promoted anti-inflammatory responses. Finally, in a STEMI population (POSTEMI; n = 272), patients had significantly higher circulating legumain before and immediately after percutaneous coronary intervention compared with healthy controls (n = 67), and high levels were associated with improved outcome.Conclusions: Our data demonstrate for the first time that legumain is upregulated during acute cardiovascular events and is associated with improved outcome.
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| 5. |
- Norman, Sven, 1984-
(författare)
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Lake bathymetry as driver of salmonid population size structure and biomass
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Most fish species undergo ontogenetic niche shifts from feeding on pelagic zooplankton, to larger benthic invertebrates and in some cases also to fish. These ontogenetic niche shifts have strong impact on the interactions within and between species, with effects on individual growth, population abundance and food web dynamics. The productivity of northern lakes is mainly controlled by light-limited primary production in benthic habitats, highlighting the importance of lake bathymetry for the abundance of benthic algae feeding macroinvertebrates, which is an important resource for fish. Theory predicts that variation in fish size structure and biomass can arise due to size-dependent differences in competitive abilities between juvenile and adults in each of their niches and by variation in niche- and habitat-specific resource production i.e. pelagic zooplankton and benthic macroinvertebrates.In this thesis, using gradient studies in mountain lakes, I studied how habitat-specific production and lake bathymetry variation affect growth, size structure and biomass in Arctic char and brown trout populations. Results showed that lake bathymetry determine the benthic contribution to whole lake primary production and the degree of ontogenetic niche shift from zooplankton to macroinvertebrates. In correspondence with theory, production of Arctic char and brown trout were related to stage- and habitat-specific gross primary production (GPP) as an increased benthic contribution to whole lake GPP in general increased individual size, population production and biomasses. Lake bathymetry also influenced the niche shift to piscivory in brown trout as reliance on piscivory were higher in relatively deep lakes more dominated by Arctic char. Finally, in a model approach, responses to different size selective harvest regulations showed that the size structure of Arctic char were more sensitive to fishing in shallow than in deep lakes. Size regulations protecting both smaller and the largest adults were shown to best preserve size structure, especially in shallower lakes. Collectively, these results contribute to the understanding of how variation in productivity and availability of stage- and habitat-specific resources and the presence of ontogenetic niche shifts affect the growth, size structure and biomass of fish. Specifically, the results highlighted the importance of shallow benthic habitats for individual size and biomass of salmonids in mountain lakes and suggests that management strategies based on relationships between lake bathymetry and population size structure and biomass could be a simple approach for sustainable management of lake salmonid population.
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| 6. |
- Quaglia, Federica, et al.
(författare)
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DisProt in 2022 : improved quality and accessibility of protein intrinsic disorder annotation
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:D1, s. D480-D487
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Tidskriftsartikel (refereegranskat)abstract
- The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.
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