| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Bogetofte, Helle, et al.
(författare)
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PARK2 mutation causes metabolic disturbances and impaired survival of human iPSC-derived neurons
- 2019
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Ingår i: Frontiers in Cellular Neuroscience. - : Frontiers Media SA. - 1662-5102. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- The protein parkin, encoded by the PARK2 gene, is vital for mitochondrial homeostasis, and although it has been implicated in Parkinson’s disease (PD), the disease mechanisms remain unclear. We have applied mass spectrometry-based proteomics to investigate the effects of parkin dysfunction on the mitochondrial proteome in human isogenic induced pluripotent stem cell-derived neurons with and without PARK2 knockout (KO). The proteomic analysis quantified nearly 60% of all mitochondrial proteins, 119 of which were dysregulated in neurons with PARK2 KO. The protein changes indicated disturbances in oxidative stress defense, mitochondrial respiration and morphology, cell cycle control, and cell viability. Structural and functional analyses revealed an increase in mitochondrial area and the presence of elongated mitochondria as well as impaired glycolysis and lactate-supported respiration, leading to an impaired cell survival in PARK2 KO neurons. This adds valuable insight into the effect of parkin dysfunction in human neurons and provides knowledge of disease-related pathways that can potentially be targeted for therapeutic intervention.
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| 3. |
- Meyer, Astrid, et al.
(författare)
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A fertile peatland forest does not constitute a major greenhouse gas sink
- 2013
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 10, s. 7739-7758
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Tidskriftsartikel (refereegranskat)abstract
- Afforestation has been proposed as a strategy to mitigate the often high greenhouse gas (GHG) emissions from agricultural soils with high organic matter content. However, the carbon dioxide (CO2) and nitrous oxide (N2O) fluxes after afforestation can be considerable, depending predominantly on site drainage and nutrient availability. Studies on the full GHG budget of afforested organic soils are scarce and hampered by the uncertainties associated with methodology. In this study we etermined the GHG budget of a spruce-dominated forest on a drained organic soil with an agricultural history. Two different approaches for determining the net ecosystem CO2 exchange (NEE) were applied, for the year 2008, one direct (eddy covariance) and the other indirect (analyzing the different components of the GHG budget), so that uncertainties in each method could be evaluated. The annual tree production in 2008 was 8.3±3.9 tC ha−1 yr−1 due to the high levels of soil nutrients, the favorable climatic conditions and the fact that the forest was probably in its phase of maximum C assimilation or shortly past it. The N2O fluxes were determined by the closed-chamber technique and amounted to 0.9±0.8 tCeq ha−1 yr−1. According to the direct measurements from the eddy covariance technique, the site acts as a minor GHG sink of −1.2±0.8 t Ceq ha−1 yr−1. This contrasts with the NEE estimate derived from the indirect approach which suggests that the site is a net GHG emitter of 0.6±4.5 tCeq ha−1 yr−1. Irrespective of the approach applied, the soil CO2 effluxes counter large amounts of the C sequestration by trees. Due to accumulated uncertainties involved in the indirect approach, the direct approach is considered the more reliable tool. As the rate of C sequestration will likely decrease with forest age, the site will probably become a GHG source once again as the trees do not compensate for the soil C and N losses. Also forests in younger age stages have been shown to have lower C assimilation rates; thus, the overall GHG sink potential of this afforested nutrient-rich organic soil is probably limited to the short period of maximum C assimilation.
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| 4. |
- Primmer, Eeva, et al.
(författare)
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Mapping Europe's institutional landscape for forest ecosystem service provision, innovations and governance
- 2021
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Ingår i: Ecosystem Services. - : Elsevier BV. - 2212-0416. ; 47
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Tidskriftsartikel (refereegranskat)abstract
- There has been a strong quest for mapping and assessing ecosystem services (ES) to support governance. Yet, the institutional landscape that governs ES provision across multiple contexts has received less attention. We fill this research gap by developing and operationalising a framework for the analysis of policy documents that address European forest ES provision. By coding and analysing references to forest ES as well as innovations and governance mechanisms addressing these ES in national strategies on forest, biodiversity and bioeconomy, we map the institutional landscape of forest ES provision in Europe. We further analyse how biophysical supply of forest ES is connected to policies paying attention to ES and identifying innovations and governance for their provision. Innovations identified in policies centre around value chains of wood and bioenergy or biodiversity conservation, while non-wood forest products, cultural heritage, and recreation receive little attention. Biophysical supply of provisioning ES is connected to policies emphasising many innovations, while little supply of regulating ES could trigger service innovations and several new governance mechanisms. As forest ecosystems have received much attention in global, European and national sustainability policies, our institutional mapping illustrates that there is room for more use of innovations in promoting ES provision.
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| 5. |
- Varumo, Liisa, et al.
(författare)
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D 2.2 Mapping of forest ecosystem services and institutional frameworks : Final report
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Promoting or upscaling governance and business innovations requires an understanding about the conditions and contexts that support a particular innovation. Indeed, context can importantly condition the emergence of new ideas as well as their stabilization and system-level uptake. Ecosystems and the services they provide can be considered this kind of context for innovations because they vary across the landscape. Furthermore, the ways in which ecosystem services (ES) are governed can importantly condition the emergence and up-take of new ideas. These institutional, structural and procedural conditions vary across different administrative units, for example countries or regions. As both ecological and institutional context matters for innovations in the forest sector, we capture these variations and provide a basis for a more context-relevant analysis of innovation evolution, which potentially supports replication and upscaling of innovations. In general, there is a good spatial understanding of Europe’s forest ecosystem services (FES) but ecosystem service supply and demand have been matched only as rough estimates of scarcity. What is missing so far is a thorough analysis of the societal demand for FES, as expressed in policy, and the combination of biophysical and institutional mapping. We propose that societal demand can be derived from formal goals and argumentation in public strategies and laws, as these are the results of processes engaging societal actors and expertise. In the past years, several European policies have gradually taken up the notion of ES, and the European Forest Strategy fares well in its reference and integration of ES. However, what is missing is an analysis of the extent and the ways in which national forest related policies recognise FES and how this recognition coincides with ecosystem service supply at the spatial scale. By analysing how different EU, national and regional policies address forest ecosystem service relevant innovations, governance mechanisms and actors, we develop a deeper understanding of the biophysical-institutional landscape that can condition innovation in the forest sector. Based on our biophysical and institutional mapping, InnoForESt can identify niche innovations and their transferability, upscaling and further co-learning in comparable high potential context regions. This report describes the justification for mapping specific FES and policies and reports the methods applied in conducting the biophysical and institutional mapping as well as the findings. The report is supplemented by a coarse level map interface that can be used to visually analyse the coincidence of biophysical FES supply and institutional FES demand, innovations and governance, as expressed in forest strategies. The biophysical mapping of FES conducted for this report focused on the supply of ES and relied on simple mapping methods. The mapping process followed four main steps: 1) Identification of FES; 2) Definition of the indicators to map the selected FES; 3) Production of Pan-European maps of selected FES, 4) analysis of hotspots, synergies and trade-offs and spatial bundles of FES. Given the European focus of the study, the identification of FES and definition of related indicators built on the CICES classification and the set of MAES indicators. Indicators were then refined based on the availability of adequate spatially-explicit data at the European level. A total of 13 indicators were eventually defined and maps produced for each of these. As maps of FES showed ES supply on a per unit area basis, the potential of a region or a country to provide a given FES requires considering the actual extent of forests in that region or country. The analysis of hotspots, synergies and trade-offs and bundles of FES, which was carried out on a subset of eight FES, allows policy makers to get further insights about FES concentrations and coincidence. Deliverable 2.2 InnoForESt 6 The institutional mapping was carried out to identify current and future policy demand for ES. The policy demand was analysed through detailed policy document analysis, for which a protocol and database were developed and iterated among the team. The initial document analysis conducted in 2018 covered the most relevant national or regional forest, biodiversity and bio-economy strategies in the InnoForESt case study areas and at the EU level, altogether 31 policy documents. The document analysis was reported through an online survey that was used to produce a database, with both quantitative grading of weight in the document and qualitative text examples. The document analysis focused on ten FES: wood, bioenergy, non-wood forest products, game, biodiversity conservation, erosion and water protection, climate regulation, resilience, cultural heritage, recreation. Additionally, the analysis considered innovation type and stage, actor responsibilities and rights as well as new governance mechanisms, for all these ten FES. Our analysis illustrates that both the biophysical distribution of FES and the policy targeting FES differ across Europe. The analysis of biophysical FES supply through bundles shows that biophysical FES tend to be related to the climatic-ecological gradient, with cultural-agricultural FES being concentrated in the Mediterranean area, wood and water FES in the central area, soil carbon FES in the northernmost area and a mix of all FES in the north-eastern area. In terms of demand for FES, our analysis shows that countries do differ in how much weight they place on different FES in their strategies. Wood and bioenergy stand out as the focal FES for both forest and bio-economy policies, while biodiversity conservation is the only FES that is in some form mentioned in all analysed policy documents. The documents identify innovations, actor roles and governance mechanisms in detail for those ecosystem services that they directly address. The analysis of policies shows that biodiversity conservation is supported with innovations. New product ideas are about wood and biomass, sometimes recognising a long value chain. Also networking innovations and market-based rearrangements centre on procurement of raw material, recognising the responsibilities and rights of industry and land-owners. With our analysis combining data on FES provision across the European landscape and document analysis of European forest, biodiversity and bio-economy policies, we show that there is a slight tendency in policies to address and detail innovations and governance for scarce forest ecosystem services. By analysing how different EU, national and regional policies address different forest relevant innovations, governance mechanisms and actors our analysis provides a deeper understanding of the biophysical-institutional landscape that can condition innovation in the forest sector, and ideally, identify opportunities for transferring and upscaling innovations.
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| 6. |
- Windhager, Jonas, et al.
(författare)
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An end-to-end workflow for multiplexed image processing and analysis
- 2023
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Ingår i: Nature Protocols. - : Springer Nature. - 1754-2189 .- 1750-2799. ; 18:11, s. 3565-3613
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Tidskriftsartikel (refereegranskat)abstract
- Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological molecules in tissues at single-cell resolution. Extracting biologically relevant information, such as the spatial distribution of cell phenotypes from multiplexed tissue imaging data, involves a number of computational tasks, including image segmentation, feature extraction and spatially resolved single-cell analysis. Here, we present an end-to-end workflow for multiplexed tissue image processing and analysis that integrates previously developed computational tools to enable these tasks in a user-friendly and customizable fashion. For data quality assessment, we highlight the utility of napari-imc for interactively inspecting raw imaging data and the cytomapper R/Bioconductor package for image visualization in R. Raw data preprocessing, image segmentation and feature extraction are performed using the steinbock toolkit. We showcase two alternative approaches for segmenting cells on the basis of supervised pixel classification and pretrained deep learning models. The extracted single-cell data are then read, processed and analyzed in R. The protocol describes the use of community-established data containers, facilitating the application of R/Bioconductor packages for dimensionality reduction, single-cell visualization and phenotyping. We provide instructions for performing spatially resolved single-cell analysis, including community analysis, cellular neighborhood detection and cell-cell interaction testing using the imcRtools R/Bioconductor package. The workflow has been previously applied to imaging mass cytometry data, but can be easily adapted to other highly multiplexed imaging technologies. This protocol can be implemented by researchers with basic bioinformatics training, and the analysis of the provided dataset can be completed within 5-6 h. An extended version is available at https://bodenmillergroup.github.io/IMCDataAnalysis/. The protocol describes the analysis of data generated by highly multiplexed tissue imaging approaches, such as imaging mass cytometry. The presented workflow includes steps for imaging data visualization, data preprocessing, image segmentation, single-cell feature extraction, reading data into R, spillover correction, quality control, cell phenotyping and spatially resolved single-cell analysis.The software packages used include napari, steinbock, DeepCell/Mesmer, Ilastik, CellProfiler, cytomapper and imcRtools. An integrated workflow for multiplexed tissue image processing and analysis, including interactive inspection of raw data, cell segmentation, feature extraction, single-cell analysis and spatial analysis.
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