| 51. |
- Lee, Yunsung, et al.
(författare)
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Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina MethylationEPIC BeadChip (EPIC). Thus, it remains unclear to what extent EPIC contributes to increased precision and accuracy in the prediction of chronological age. Results: We developed three blood-based epigenetic clocks for human adults using EPIC-based DNA methylation (DNAm) data from the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Gene Expression Omnibus (GEO) public repository: 1) an Adult Blood-based EPIC Clock (ABEC) trained on DNAm data from MoBa (n = 1592, age-span: 19 to 59 years), 2) an extended ABEC (eABEC) trained on DNAm data from MoBa and GEO (n = 2227, age-span: 18 to 88 years), and 3) a common ABEC (cABEC) trained on the same training set as eABEC but restricted to CpGs common to 450 K and EPIC. Our clocks showed high precision (Pearson correlation between chronological and epigenetic age (r) > 0.94) in independent cohorts, including GSE111165 (n = 15), GSE115278 (n = 108), GSE132203 (n = 795), and the Epigenetics in Pregnancy (EPIPREG) study of the STORK Groruddalen Cohort (n = 470). This high precision is unlikely due to the use of EPIC, but rather due to the large sample size of the training set. Conclusions: Our ABECs predicted adults’ chronological age precisely in independent cohorts. As EPIC is now the dominant platform for measuring DNAm, these clocks will be useful in further predictions of chronological age, age-related diseases, and mortality.
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| 52. |
- Lennartsson, Tommy, et al.
(författare)
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Diversity in Ecological and Social Contexts
- 2018
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Ingår i: Issues and Concepts in Historical Ecology. - Cambridge : Cambridge University Press. - 9781108420983 - 9781108355780 ; , s. 182-239
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Konferensbidrag (refereegranskat)
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| 53. |
- Lien, Sigbjorn, et al.
(författare)
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The Atlantic salmon genome provides insights into rediploidization
- 2016
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 533:7602, s. 200-205
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Tidskriftsartikel (refereegranskat)abstract
- The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
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| 54. |
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| 55. |
- Lindgren, Åsa, et al.
(författare)
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Defense mechanisms against grazing : a study of trypsin inhibitor responses to simulated grazing by the sedge Carex bigelowii
- 2007
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Ingår i: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 116:9, s. 1540-1546
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Tidskriftsartikel (refereegranskat)abstract
- Trypsin inhibitors have been suggested to constitute an inducible defense in the sedge Carex bigelowii, and some former studies suggest that this might be a cause for the cyclic population dynamics in many alpine and arctic small mammals, for example lemmings (Lemmus lemmus). We investigated this further by using a method of simulated grazing (clipping) at different intensities, in three different habitats with varying resource availability, with different harvest times (hours after clipping), and two different stages of ramets (reproductive/vegetative) in a study from the Swedish mountain range. Our results do not indicate that C. bigelowii has an inducible defense constituted by an increase in trypsin inhibitor activity (TIA), but rather that the amount of soluble plant proteins (SPP) is lowered in wounded plants. The responses were somewhat different in the three habitats, with ramets growing in the marsh showing the highest ratio of TIA to SPP, due to low amounts of SPP. We did not find any significant effects of harvest time, or of the stage of the ramet that could support the hypothesis of an inducible defense. To conclude, we could not find any evidence for an inducible defense consisting of trypsin inhibitors in Carex bigelowii ramets, but we did find variations in the amount of SPP that may have nutritional consequences for herbivores.
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| 56. |
- Lindgren, Åsa, 1973-
(författare)
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Effects of herbivory on arctic and alpine vegetation
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The distribution of plant species and functional traits in alpine and arctic environments are determined by abiotic conditions, but also by biotic interactions. In this thesis, I investigate interactions among plants and herbivory effects on plant community composition and plant functional traits in three different regions: Swedish Lapland, Beringia (USA/Russia) and Finnmark (Norway). Reindeer grazing was found to be extensive in southern Lapland and had limited effects on plant community composition and seedling germination. However, reindeer presence was found to influence plant functional traits, particularly in the subalpine birch forest. Tall herbs were lower and had lower SLA when reindeer were present, while small herbs showed an opposite pattern. The contrasting effects on the two herb groups are probably explained by a competitive release for small herbs when the tall herbs are suppressed by reindeer. Rodents had the largest relative impact on plant community composition in southern Lapland and this is consistent with the study from Finnmark, where rodents heavily affected dwarf shrubs on predator-free islands. With no predators present, vole densities increased profoundly and almost depleted some dwarf shrub species. These results support the idea that small mammals in arctic and alpine tundra are controlled by predators (i.e. top-down). However, a decrease in the nutritional quality in a sedge after defoliation gives support for the idea that small mammals are regulated by plant quality (i.e. bottom-up). In Beringia, small and large herbivores differed in the relation to plant community composition, since large herbivores were related to species richness and small herbivores were related to plant abundance. Plant functional traits were related only to large herbivores and standing crop of vascular plants.
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| 57. |
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| 58. |
- Lindgren, Åsa, et al.
(författare)
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The impact of disturbance and seed availability on germination in alpine vegetation in the Scandinavian mountains
- 2007
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Ingår i: Arctic, Antarctic and Alpine research. - Colorado : Institute of Arctic and Alpine Research, University of Colorado. - 1523-0430 .- 1938-4246. ; 39:3, s. 449-454
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Tidskriftsartikel (refereegranskat)abstract
- The availability of seeds and microsites are limiting factors for many plant species of different vegetation types. We have investigated the existence of such limitations in two habitats, an alpine heath and a subalpine birch forest, where abiotic factors are hypothesized to be the main determining factor of plant species distributions. Both habitats are characterized by a short growing season and cold temperatures, and the alpine heath is also constrained by low productivity. A seed addition experiment including six vascular plants, selected by different functional traits and occurrence, showed that seed limitation was an important factor in these habitats. Removal of the aboveground biomass (controlled disturbance) increased germination only for some species. The effect of reindeer presence was found to be of less importance, probably due to low and varying densities of reindeer. To conclude, we found that seed limitation was the most important factor limiting the distribution of our studied species in the two alpine environments.
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| 59. |
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| 60. |
- Maes, Joachim, et al.
(författare)
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An indicator framework for assessing ecosystem services in support of the EU Biodiversity Strategy to 2020
- 2016
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Ingår i: Ecosystem Services. - : Elsevier. - 2212-0416. ; 17, s. 14-23
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Tidskriftsartikel (refereegranskat)abstract
- In the EU, the mapping and assessment of ecosystems and their services, abbreviated to MAES, is seen as a key action for the advancement of biodiversity objectives, and also to inform the development and implementation of related policies on water, climate, agriculture, forest, marine and regional planning. In this study, we present the development of an analytical framework which ensures that consistent approaches are used throughout the EU. It is framed by a broad set of key policy questions and structured around a conceptual framework that links human societies and their well-being with the environment. Next, this framework is tested through four thematic pilot studies, including stakeholders and experts working at different scales and governance levels, which contributed indicators to assess the state of ecosystem services. Indicators were scored according to different criteria and assorted per ecosystem type and ecosystem services using the common international classification of ecosystem services (CICES) as typology. We concluded that there is potential to develop a first EU wide ecosystem assessment on the basis of existing data if they are combined in a creative way. However, substantial data gaps remain to be filled before a fully integrated and complete ecosystem assessment can be carried out.
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