| 1. |
- Craddock, Nick, et al.
(författare)
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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7289, s. 713-720
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Tidskriftsartikel (refereegranskat)abstract
- Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed,19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated similar to 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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| 2. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 3. |
- Rich, Rebecca L., et al.
(författare)
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A global benchmark study using affinity-based biosensors
- 2009
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Ingår i: Analytical Biochemistry. - : Elsevier BV. - 0003-2697 .- 1096-0309. ; 386:2, s. 194-216
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Tidskriftsartikel (refereegranskat)abstract
- To explore the variability in biosensor studies, 150 participants from 20 countries were given the same protein samples and asked to determine kinetic rate constants for the interaction. We chose a protein system that was amenable to analysis using different biosensor platforms as well as by users of different expertise levels. The two proteins (a 50-kDa Fab and a 60-kDa glutathione S-transferase [GST] antigen) form a relatively high-affinity complex, so participants needed to optimize several experimental parameters, including ligand immobilization and regeneration conditions as well as analyte concentrations and injection/dissociation times. Although most participants collected binding responses that could be fit to yield kinetic parameters, the quality of a few data sets could have been improved by optimizing the assay design. Once these outliers were removed, the average reported affinity across the remaining panel of participants was 620 pM with a standard deviation of 980 pM. These results demonstrate that when this biosensor assay was designed and executed appropriately, the reported rate constants were consistent, and independent of which protein was immobilized and which biosensor was used.
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| 4. |
- Farnocchia, Davide, et al.
(författare)
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The Second International Asteroid Warning Network Timing Campaign: 2005 LW3
- 2023
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Ingår i: The Planetary Science Journal. - : Institute of Physics (IOP). - 2632-3338. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- The Earth close approach of near-Earth asteroid 2005 LW3 on 2022 November 23 represented a good opportunity for a second observing campaign to test the timing accuracy of astrometric observation. With 82 participating stations, the International Asteroid Warning Network collected 1046 observations of 2005 LW3 around the time of the close approach. Compared to the previous timing campaign targeting 2019 XS, some individual observers were able to significantly improve the accuracy of their reported observation times. In particular, U.S. surveys achieved good timing performance. However, no broad, systematic improvement was achieved compared to the previous campaign, with an overall negative bias persisting among the different observers. The calibration of observing times and the mitigation of timing errors should be important future considerations for observers and orbit computers, respectively.
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| 5. |
- Lundgren, Veronica, et al.
(författare)
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Metabolic and physiological changes in Prymnesium parvum when grown under, and grazing on prey of, variable nitrogen:phosphorus stoichiometry
- 2016
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Ingår i: Harmful Algae. - : Elsevier BV. - 1568-9883 .- 1878-1470. ; 55, s. 1-12
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Tidskriftsartikel (refereegranskat)abstract
- Mixotrophy is found in almost all classes of phytoplankton in a wide range of aquatic habitats ranging from oligotrophic to eutrophic marine and freshwater systems. Few studies have addressed how the nutritional status of the predator and/or the prey affects mixotrophic metabolism despite the realization that mixotrophy is important ecologically. Laboratory experiments were conducted to examine changes in growth rates and physiological states of the toxic haptophyte Prymnesium parvum when fed Rhodomonas sauna of varying nutritional status. Haemolytic activity of P. parvum and prey mortality of R. sauna were also measured. P. parvum cultures grown to be comparatively low in nitrogen (low-N), phosphorus (low-P) or low in both nutrients (low-NP) were mixed with low-NP, low-N, and low-P R. saline in all possible combinations, i.e., a 3 x 3 factorial design. N deficiency was obtained in the low-N cultures, while true P deficiency may not have been obtained in the low-P cultures. Mortality rates of R. salina (both due to ingestion and/or cell rupture as a function of grazing or toxic effects) were higher when R. sauna cells were low-P, N-rich, regardless of the nutritional state of P. parvum. Mortality rates were, however, directly related to the initial prey:predator cell ratios. On the other hand, growth of the predator was a function of nutritional status and a significant positive correlation was observed between growth rates of P. parvum and cell-specific depletion rates of N, whereas no such relationship was found between P. parvum growth rates and depletion rates of P. In addition, the greatest changes in chlorophyll content and stoichiometric ratios of P. parvum were observed in high N:P conditions. Therefore, P. parvum may show enhanced success under conditions of higher inorganic N:P, which are likely favored in the future due to increases in eutrophication and altered nutrient stoichiometry driven by anthropogenic nutrient loads that are increasingly enriched in N relative to P. (C) 2016 Elsevier B.V. All rights reserved.
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| 6. |
- Mitra, Aditee, et al.
(författare)
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Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition : Incorporation of Diverse Mixotrophic Strategies
- 2016
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Ingår i: Protist. - : Elsevier BV. - 1434-4610 .- 1618-0941. ; 167:2, s. 106-120
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Tidskriftsartikel (refereegranskat)abstract
- Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic "phytoplankton" and phagotrophic "microzooplankton". However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an ecophysiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks. (C) 2016 The Authors. Published by Elsevier GmbH.
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| 7. |
- Flynn, Kevin J, et al.
(författare)
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Misuse of the phytoplankton-zooplankton dichotomy : the need to assign organisms as mixotrophs within plankton functional types
- 2013
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Ingår i: Journal of Plankton Research. - : Oxford University Press (OUP). - 0142-7873 .- 1464-3774. ; 35:1, s. 3-11
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Tidskriftsartikel (refereegranskat)abstract
- The classic portrayal of plankton is dominated by phytoplanktonic primary producersand zooplanktonic secondary producers. In reality, many if not most planktontraditionally labelled as phytoplankton or microzooplankton should be identifiedas mixotrophs, contributing to both primary and secondary production. Mixotrophicprotists (i.e. single-celled eukaryotes that perform photosynthesis and grazeon particles) do not represent a minor component of the plankton, as some formof inferior representatives of the past evolution of protists; they represent a majorcomponent of the extant protist plankton, and one which could become moredominant with climate change. The implications for this mistaken identification, ofthe incorrect labelling of mixotrophs as “phytoplankton” or “microzooplankton”,are great. It extends from the (mis)use of photopigments as indicators of primaryproduction performed by strict photoautotrophs rather than also (co)locating mixotrophicactivity, through to the inadequacy of plankton functional type descriptionsin models (noting that mixotrophic production in the individual organism is not asimple sum of phototrophy and heterotrophy). We propose that mixotrophy shouldbe recognized as a major contributor to plankton dynamics, with due effortexpended in field and laboratory studies, and should no longer be side-lined inconceptual food webs or in mathematical models.
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| 8. |
- Mayers, Joshua, 1988, et al.
(författare)
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An approaching global phosphorus crisis and microalgal biotechnology: A growing problem & strategies for effective use
- 2015
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Phosphorus (P) is a critical element for life on Earth. However, readily extractable ores are being exhausted rapidly and a combination of increasing usage, rising costs and numerous geopolitical problems are expected to impact food security and industry sectors within the next few decades. This hence represents another great anthropogenic challenge and near-future issue. P is needed in the production of microalgal biomass; indeed the value of P in microalgae is similar or exceeds that of the potential biofuels, demanding a 100% recovery and recycling of P. However, unlike nitrogen (N) sources (that can be synthesised) for which the relationship of cell-contents and growth is linear, the need for P is less clearly understood. We have empirically explored the interaction between P supply and microalgal production and biochemical composition. P usage could be at least halved relative to the use of N, while maintaining adequate growth of Nannochloropsis. Indeed, by deploying certain strategies, the amount of P required to produce 1 kg of biomass can be decreased from 2.4 g to 0.85 g (65% reduction). The quantitative effects of dual N- and P-limitation on biochemical composition, fatty acid profile and biodiesel quality were also evaluated in a greater detail than has previously been reported. The replacement of inorganic nutrients with those obtained from waste nutrient streams was examined and also proved to be a successful strategy in decreasing resource consumption. P usage in the broader context of large-scale microalgal cultivation will be put into context with information critical for algal physiology, practitioners and LCA development.
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| 9. |
- Mayers, Joshua, 1988, et al.
(författare)
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Nutrients from anaerobic digestion effluents for cultivation of the microalga Nannochloropsis sp. - Impact on growth, biochemical composition and the potential for cost and environmental impact savings
- 2017
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Ingår i: Algal Research. - : Elsevier BV. - 2211-9264. ; 26, s. 275-286
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Tidskriftsartikel (refereegranskat)abstract
- Microalgal biotechnology has yielded a range of products for different consumer markets, but large scale production for bulk commodities is limited by the cost and environmental impact of production. Nutrient requirements for large-scale production contribute significantly to the cost and environmental impact of microalgal biomass production and should subsequently be addressed by more careful sourcing of nutrients. This study assessed the use of nitrogen and phosphorus contained in effluents from anaerobic digestion of food waste to cultivate the marine microalga Nannochloropsis sp. With suitable dilution, effluent could replace 100% of nitrogen demands and 16% of required phosphorus, without significant impacts on growth or biomass productivity. Additional phosphorus requirements could be decreased by increasing the N:P molar ratio of the media from 16:1 to 32:1. Nannochloropsis sp. accumulated lipid up to 50% of dry weight under N-stress, with significant increases in the content of saturated and mono-unsaturated fatty acids. Using empirical data generated in this study, the cost and environmental impact of nitrogen and phosphorus supply was assessed versus the use of fertilizers for biomass and biodiesel production. Nutrient requirements predicted by the Redfield Ratio overestimating impacts by as much as 140% compared to empirical data. By utilising residual nutrients and optimising nutrient supply, the cost and environmental impact of nitrogen and phosphorus were decreased by >90% versus the use of artificial fertilizers. This study demonstrates the importance of using empirical data for process evaluation and how anaerobic digestate effluent derived nutrients can contribute to the sustainability of algal biomass production.
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| 10. |
- Mitra, Aditee, et al.
(författare)
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The role of mixotrophic protists in the biological carbon pump
- 2014
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 11, s. 995-1005
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Tidskriftsartikel (refereegranskat)abstract
- The traditional view of the planktonic foodweb describes consumption of inorganic nutrientsby photo-autotrophic phytoplankton, which in turn supports zooplankton and ultimately higher trophic levels. Pathways centred on bacteria provide mechanisms for nutrient recycling. This structure lies at the foundation of most models used to explore biogeochemical cycling, functioning of the biological pump, and the impact of climate change on these processes. We suggest an alternative paradigm, which sees the bulk of the base of this foodweb supported by protist plankton (phytoplankton and microzooplankton) communities that are mixotrophic – combining phototrophy and phagotrophy within a single cell. The photoautotrophic eukaryotic plankton and their heterotrophic microzooplankton grazers dominate only within immature environments (e.g., spring bloom in temperate systems). With their flexible nutrition, mixotrophic protists dominate in more mature systems (e.g., temperate summer, established eutrophic systems and oligotrophic systems); the more stable water columns suggested under climate change may also be expected to favour these mixotrophs. We explore how such a predominantlymixotrophic structure affects microbial trophic dynamics and the biological pump. The mixotroph dominated structure differs fundamentally in its flow of energy and nutrients, with a shortened and potentially more efficient chain from nutrient regeneration to primary production. Furthermore, mixotrophy enables a direct conduit for the support of primary production from bacterial production. We show how the exclusion of an explicit mixotrophic component in studies of the pelagic microbial communities leads to a failure to capture the true dynamics of the carbon flow. In order to prevent a misinterpretation of the full implications of climate change upon biogeochemical cyclingand the functioning of the biological pump, we recommend inclusion of multi-nutrient mixotroph models within ecosystem studies.
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