| 1. |
- Kronenberg, Jakub, et al.
(författare)
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The thorny path toward greening : unintended consequences, trade-offs, and constraints in green and blue infrastructure planning, implementation, and management
- 2021
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Ingår i: Ecology & Society. - : Resilience Alliance, Inc.. - 1708-3087. ; 26:2
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Tidskriftsartikel (refereegranskat)abstract
- Urban green and blue space interventions may bring about unintended consequences, involving trade-offs between the different land uses, and indeed, between the needs of different urban inhabitants, land users, and owners. Such trade-offs include choices between green/blue and non-green/blue projects, between broader land sparing vs. land sharing patterns, between satisfying the needs of the different inhabitants, but also between different ways of arranging the green and blue spaces. We analyze investment and planning initiatives in six case-study cities related to green and blue infrastructure (GBI) through the lens of a predefined set of questions an analytical framework based on the assumption that the flows of benefits from GBI to urban inhabitants and other stakeholders are mediated by three filters: infrastructures, institutions, and perceptions. The paper builds on the authors' own knowledge and experience with the analyzed case-study cities and beyond, a literature overview, a review of the relevant city documents, and interviews with key informants. The case studies indicate examples of initiatives that were intended to make GBI benefits available and accessible to urban inhabitants, in recognition of GBI as spaces with diverse functionality. Some case studies provide examples of trade-offs in trying to plan and design a green space for multiple private and public interests in densely built-up areas. The unintended consequences most typically resulted from the underappreciation of the complexity of social-ecological systems and more specifically the complexity of the involved infrastructures, institutions, and perceptions. The most important challenges addressed in the paper include trade-offs between the different ways of satisfying the residents' different needs related to the benefits from ecosystem services, ensuring proper recognition of the inhabitants' needs and perceptions, ecogentrification, caveats related to the formalization of informal spaces, and the need to consider temporal dynamics and cross-scale approaches that compromise different goals at different geographical scales.
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| 2. |
- Uhlén, Mathias, et al.
(författare)
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A human protein atlas for normal and cancer tissues based on antibody proteomics
- 2005
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Ingår i: Molecular & Cellular Proteomics. - 1535-9476 .- 1535-9484. ; 4:12, s. 1920-1932
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Tidskriftsartikel (refereegranskat)abstract
- Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, similar to 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.
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| 3. |
- Borgström, Sara, et al.
(författare)
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Retaining multi-functionality in a rapidly changing urban landscape : insights from a participatory, resilience thinking process in Stockholm, Sweden
- 2021
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Ingår i: Ecology & Society. - : Resilience Alliance, Inc.. - 1708-3087. ; 26:4
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Tidskriftsartikel (refereegranskat)abstract
- Urban social-ecological resilience research has focused on conceptual explorations, while less attention has been paid to how resilience thinking in practice may inform urban development. Using the rapidly urbanizing landscape in Stockholm as a case, we explore the urban specifics of resilience thinking practice and thereby contribute to the development of knowledge and practice of social-ecological resilience thinking generally. The study addresses an urban wicked problem: how to ensure that people continue to have access to the means necessary to realize benefits from green blue infrastructure, when the city is changing and governance is fragmented. Drawing on insights from the design and implementation of a participatory dialogue process, we outline methodological adaptations to a resilience informed system exploration, to better accommodate the complexity of urban systems. The participatory process included three phases: basic system understanding, dealing with change over time, and identifying alternative ways forward. Different knowledge elicitation and deliberation methods were deployed within workshops, surveys, and interviews, and were paralleled by a thorough reflexive analysis of process outcomes. The main discussion points are stakeholder participation, the role of discourses, identities and mandates, agency, and adaptive capacity, and alternative strategies for dealing with change. Deep knowledge of the complexities of urban land use and governance requires the involvement of diverse stakeholders. Handling this diversity poses a challenge for process design: combining the ambition of an inclusive process and the need to be relevant with the use of bridging concepts increases the risk of reducing the level of complexity of the deliberative process. There is also a risk of participation bias, where stakeholders knowledgeable about the green blue infrastructure are easier to engage compared to stakeholders with knowledge about drivers of change and urban governance, which will influence the system understanding and envisioned alternative pathways for taking action.
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| 4. |
- Hard, Joanna, et al.
(författare)
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Conbase : a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing
- 2019
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Ingår i: Genome Biology. - : BMC. - 1465-6906 .- 1474-760X. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data. Conbase leverages phased read data from multiple samples in a dataset to achieve increased confidence in somatic variant calls and genotype predictions. Comparing the performance of Conbase to three other methods, we find that Conbase performs best in terms of false discovery rate and specificity and provides superior robustness on simulated data, in vitro expanded fibroblasts and clonal lymphocyte populations isolated directly from a healthy human donor.
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| 5. |
- He, Hongxing, 1987, et al.
(författare)
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Forests on drained agricultural peatland are potentially large sources of greenhouse gases – insights from a full rotation period simulation
- 2016
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- The CoupModel was used to simulate a Norway spruce forest on fertile drained peat over 60 years, from planting in 1951 until 2011, describing abiotic, biotic and greenhouse gas (GHG) emissions (CO2 and N2O). By calibrating the model against tree ring data a “vegetation fitted” model was obtained by which we were able to describe the fluxes and controlling factors over the 60 years. We discuss some conceptual issues relevant to improving the model in order to better understand peat soil simulations. However, the present model was able to describe the most important ecosystem dynamics such as the plant biomass development and GHG emissions. The GHG fluxes are composed of two important quantities, the spruce forest carbon (C) uptake, 413 g C m-2 yr-1 and the decomposition of peat soil, 399 gCm-2 yr-1. N2O emissions contribute to the GHG emissions by up to 0.7 gNm-2 yr-1, corresponding to 76 g Cm-2 yr-1. The 60-year old spruce forest has an accumulated biomass of 16.0 kg Cm-2 (corresponding to 60 kgCO2 m-2). However, over this period, 26.4 kg m-2 (97 kgCO2eqm-2) has been added to the atmosphere, as both CO2 and N2O originating from the peat soil and, indirectly, from forest thinning products, which we assume have a short lifetime. We conclude that after harvest at an age of 80 years, most of the stored biomass carbon is liable to be released, the system having captured C only temporarily and with a cost of disappeared peat, adding CO2 to the atmosphere.
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| 6. |
- Mageroy, Melissa H., et al.
(författare)
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Priming of inducible defenses protects Norway spruce against tree‐killing bark beetles
- 2020
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Ingår i: Plant, Cell and Environment. - : John Wiley & Sons. - 0140-7791 .- 1365-3040. ; 43:2, s. 420-430
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Tidskriftsartikel (refereegranskat)abstract
- Plants can form an immunological memory known as defense priming, whereby exposure to a priming stimulus enables quicker or stronger response to subsequent attack by pests and pathogens. Such priming of inducible defenses provides increased protection and reduces allocation costs of defense. Defense priming has been widely studied for short–lived model plants such as Arabidopsis, but little is known about this phenomenon in long‐lived plants like spruce. We compared the effects of pre‐treatment with sub‐lethal fungal inoculations or application of the phytohormone methyl jasmonate (MeJA) on the resistance of 48‐year‐old Norway spruce (Picea abies) trees to mass attack by a tree‐killing bark beetle beginning 35 days later. Bark beetles heavily infested and killed untreated trees, but largely avoided fungus‐inoculated trees and MeJA‐treated trees. Quantification of defensive terpenes at the time of bark beetle attack showed fungal inoculation induced 91‐fold higher terpene concentrations compared to untreated trees, while application of MeJA did not significantly increase terpenes. These results indicate that resistance in fungus‐inoculated trees is a result of direct induction of defenses while resistance in MeJA‐treated trees is due to defense priming. This work extends our knowledge of defense priming from model plants to an ecologically important tree species.
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| 7. |
- Zhao, Tao, et al.
(författare)
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Induced Terpene Accumulation in Norway Spruce Inhibits Bark Beetle Colonization in a Dose-Dependent Manner
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:10, s. e26649-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tree-killing bark beetles (Coleoptera, Scolytinae) are among the most economically and ecologically important forest pests in the northern hemisphere. Induction of terpenoid-based oleoresin has long been considered important in conifer defense against bark beetles, but it has been difficult to demonstrate a direct correlation between terpene levels and resistance to bark beetle colonization. Methods: To test for inhibitory effects of induced terpenes on colonization by the spruce bark beetle Ips typographus (L.) we inoculated 20 mature Norway spruce Picea abies (L.) Karsten trees with a virulent fungus associated with the beetle, Ceratocystis polonica (Siem.) C. Moreau, and investigated induced terpene levels and beetle colonization in the bark. Results: Fungal inoculation induced very strong and highly variable terpene accumulation 35 days after inoculation. Trees with high induced terpene levels (n = 7) had only 4.9% as many beetle attacks (5.1 vs. 103.5 attacks m(-2)) and 2.6% as much gallery length (0.029 m m(-2) vs. 1.11 m m(-2)) as trees with low terpene levels (n = 6). There was a highly significant rank correlation between terpene levels at day 35 and beetle colonization in individual trees. The relationship between induced terpene levels and beetle colonization was not linear but thresholded: above a low threshold concentration of similar to 100 mg terpene g(-1) dry phloem trees suffered only moderate beetle colonization, and above a high threshold of similar to 200 mg terpene g(-1) dry phloem trees were virtually unattacked. Conclusion/Significance: This is the first study demonstrating a dose-dependent relationship between induced terpenes and tree resistance to bark beetle colonization under field conditions, indicating that terpene induction may be instrumental in tree resistance. This knowledge could be useful for developing management strategies that decrease the impact of tree-killing bark beetles.
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| 8. |
- Zhao, Tao, et al.
(författare)
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The influence of Ceratocystis polonica inoculation and methyl jasmonate application on terpene chemistry of Norway spruce, Picea abies
- 2010
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Ingår i: Phytochemistry. - : Elsevier BV. - 0031-9422 .- 1873-3700. ; 71:11-12, s. 1332-1341
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Tidskriftsartikel (refereegranskat)abstract
- Constitutive and inducible terpene production is involved in conifer resistance against bark beetles and their associated fungi. In this study 72 Norway spruce (Picea abies) were randomly assigned to methyl jasmonate (MJ) application, inoculation with the bluestain fungus Ceratocystis polonica, or no-treatment control. We investigated terpene levels in the stem bark of the trees before treatment, 30 days and one year after treatment using GC-MS and two-dimensional GC (2D-GC) with a chiral column, and monitored landing and attack rates of the spruce bark beetle, Ips typographus, on the trees by sticky traps and visual inspection. Thirty days after fungal inoculation the absolute amount and relative proportion of (+)-3-carene, sabinene, and terpinolene increased and (+)-alpha-pinene decreased. Spraying the stems with MJ tended to generally increase the concentration of most major terpenes with minor alteration to their relative proportions, but significant increases were only observed for (-)-beta-pinene and (-)-limonene. Fungal inoculation significantly increased the enantiomeric ratio of (-)-alpha-pinene and (-)-limonene 1 month after treatment, whereas MJ only increased that of (-)-limonene. One year after treatment, both MJ and fungal inoculation increased the concentration of most terpenes relative to undisturbed control trees, with significant changes in (-)-beta-pinene, (-)-beta-phellandrene and some other compounds. Terpene levels did not change in untreated stem sections after treatment, and chemical induction by MJ and C polonica thus seemed to be restricted to the treated stem section. The enantiomeric ratio of (-)-alpha-pinene was significantly higher and the relative proportions of ( -)-limonene were significantly lower in trees that were attractive to bark beetles compared to unattractive trees. One month after fungal inoculation, the total amount of diterpenes was significantly higher in putative resistant trees with shorter lesion lengths than in putative susceptible trees with longer lesions. Thus, terpene composition in the stem bark may be related to resistance of Norway spruce against I. typographus and C. polonica.
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