Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Endogenous regime change : Lessons from transition pathways in Dutch dairy farming
    Runhaar, Hens ; Fünfschilling, Lea ; Pol-Van Dasselaar, Agnes van den; Moors, Ellen H.M. ; Temmink, Rani ; Hekkert, Marko - \ 2020
    Environmental Innovation and Societal Transitions 36 (2020). - ISSN 2210-4224 - p. 137 - 150.
    Governance - Grazing - Institutional logics - Productivist agriculture - The Netherlands - Transformation

    Sustainability transitions are commonly considered impossible without regime change. Theoretical work on regime change has mainly focused on niches and landscapes and less on change ‘from within’. Empirical analysis helps theorising endogenous regime change. Conceptualising regimes as semi-coherent entities composed of multiple ‘institutional logics’, we analyse the endogenous regime change in Dutch dairy farming. Practices in this sector have become more and more market-driven. This dominant logic however was increasingly challenged by institutional logics centring round cultural identity and sustainability. Tensions particularly centred round the increased indoor housing of cows. The contestation of this practice eventually led to a first ‘crack’ in the regime, as it weakened the dominance of the market logic and enabled opportunities for more sustainability. Our case study shows that the presence of alternative institutional logics is necessary to crack the regime, but opportunities to patch it back together are similarly crucial to enable sustainability transitions.

    Season-specific carryover of early life associations in a monogamous bird species
    Kurvers, Ralf H.J.M. ; Prox, Lea ; Farine, Damien R. ; Jongeling, Coretta ; Snijders, Lysanne - \ 2020
    Animal Behaviour 164 (2020). - ISSN 0003-3472 - p. 25 - 37.
    aggression - early life - familiarity - genetic relatedness - monogamous - pair formation - social associations - social relationships

    Social relationships can have important fitness consequences. Although there is increasing evidence that social relationships carry over across contexts, few studies have investigated whether relationships formed early in life are carried over to adulthood. For example, juveniles of monogamous species go through a major life history stage transition, pair formation, during which the pair bond becomes a central unit of the social organization. At present, it remains unclear whether pair members retain their early life relationships after pair formation. We investigated whether same-sex associations formed early in life carry over into adulthood and whether carryover was dependent on season, in a monogamous species. We also investigated the role of familiarity, genetic relatedness and aggression on the perseverance of social associations. We studied the social structure before and after pair formation in captive barnacle geese, Branta leucopsis, a highly social, long-lived, monogamous species. We constructed association networks of groups of geese before pair formation, during the subsequent breeding season and in the following wintering season. Next, we studied how these associations carried over during seasonal changes. We found that early life associations in females were lost during the breeding season but resurfaced during the subsequent wintering season. In males, the early life associations persisted across both seasons. Association persistence was not mediated by genetic relatedness or familiarity. The high level of aggressiveness of males, but not females, in the breeding season suggests that males may have played a key role in shaping both their own social environment and that of their partners. We show that early life social relationships can be maintained well into later life. Such relationships can be sustained even if they are temporarily disrupted, for example due to reproductive behaviour. Our findings therefore highlight that the early life social environment can have lifelong consequences for individuals’ social environment.

    Post-fire management treatment effects on soil properties and burned area restoration in a wildland-urban interface, Haifa Fire case study
    Wittenberg, Lea ; Wal, Hilde van der; Keesstra, Saskia ; Tessler, Naama - \ 2020
    Science of the Total Environment 716 (2020). - ISSN 0048-9697
    Ash - Post-fire management - Soil - Water repellency - Wildland-urban interface

    In November 2016, the urban dry streams (wadis) of the city of Haifa in Northern Israel were on fire. However, it was not just the fire that was threatening urban areas. Post-fire precipitation could turn into urban floods, further aggravating the fire damages. Several months after the fire a considerable restoration effort was initiated to restore the burned areas and mitigate future events. For urban forests the rehabilitation strategy was planned and implemented according to the topographic structure of the burned site and anticipated soil erosion. Accordingly, various post-fire management techniques were used: salvage-logging, afforestation, log erosion barriers and coconut fibre-webs. This study aimed to look at the effects of these methods on soil properties, namely, gravimetrical soil moisture, soil organic matter content, pH, electrical conductivity, hydraulic conductivity and soil water repellency. Results indicate that the control (burned, non-managed) site was the highest in soil moisture, organic matter and electrical conductivity compared to all other sites, however, the existence of ash cover made the response to precipitation unpredictable. The hydraulic conductivity (K) of the black ash (24.1 ± 8.6 mm/h), the white ash (19.0 ± 10.7 mm/h) and the disturbed (mixed) ash (11.7 ± 3.7 mm/h) were significantly higher than the underlying soil (3.3 ± 0.7 mm/h). As a result of these differences in K value, precipitation only infiltrates through the ash layers and then flows along the interface of the ash and the soil, triggering soil erosion. Most of the sites that were salvage logged showed signs of erosion. The log barriers were only effective for downstream areas. The afforestation could help to homogenise the soil, but the vegetation cover would be less dense and stable than after natural reforestation. Furthermore, the coconut fibre webs helped to improve the soil water retention and decreased the direct impact of rainfall.

    Absolute quantitation of microbes using 16S rRNA gene metabarcoding : A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike-in standard
    Zemb, Olivier ; Achard, Caroline S. ; Hamelin, Jerome ; Almeida, Marie Léa De; Gabinaud, Béatrice ; Cauquil, Laurent ; Verschuren, Lisanne M.G. ; Godon, Jean Jacques - \ 2020
    MicrobiologyOpen 9 (2020)3. - ISSN 2045-8827
    16S rRNA gene - absolute count data - metabarcoding - microbiome - normalization - spike-in

    Metabarcoding of the 16S rRNA gene is commonly used to characterize microbial communities, by estimating the relative abundance of microbes. Here, we present a method to retrieve the concentrations of the 16S rRNA gene per gram of any environmental sample using a synthetic standard in minuscule amounts (100 ppm to 1% of the 16S rRNA sequences) that is added to the sample before DNA extraction and quantified by two quantitative polymerase chain reaction (qPCR) reactions. This allows normalizing by the initial microbial density, taking into account the DNA recovery yield. We quantified the internal standard and the total load of 16S rRNA genes by qPCR. The qPCR for the latter uses the exact same primers as those used for Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene to increase accuracy. We are able to calculate the absolute concentration of the species per gram of sample, taking into account the DNA recovery yield. This is crucial for an accurate estimate as the yield varied between 40% and 84%. This method avoids sacrificing a high proportion of the sequencing effort to quantify the internal standard. If sacrificing a part of the sequencing effort to the internal standard is acceptable, we however recommend that the internal standard accounts for 30% of the environmental 16S rRNA genes to avoid the PCR bias associated with rare phylotypes. The method proposed here was tested on a feces sample but can be applied more broadly on any environmental sample. This method offers a real improvement of metabarcoding of microbial communities since it makes the method quantitative with limited efforts.

    The impact of pectin supplementation on intestinal barrier function in healthy young adults and healthy elderly
    Wilms, Ellen ; Jonkers, Daisy M.A.E. ; Savelkoul, Huub F.J. ; Elizalde, Montserrat ; Tischmann, Lea ; Vos, Paul de; Masclee, Ad A.M. ; Troost, Freddy J. - \ 2019
    Nutrients 11 (2019)7. - ISSN 2072-6643
    Aging - Defense - Dietary fiber - Gastrointestinal - Intestinal permeability - Tight junctions - Tolerance

    Intestinal barrier function is suggested to decrease with aging and may be improved by pectin intake. The aim of this study was to investigate the e ects of four weeks pectin supplementation on gastrointestinal barrier function in vivo and ex vivo in di erent age groups. In a randomized, double-blind, placebo-controlled, parallel study, 52 healthy young adults (18–40 years) and 48 healthy elderly (65–75 years) received 15 g/day pectin or placebo for four weeks. Pre- and post-intervention, in vivo gastrointestinal permeability by a multisugar test, and defense capacity in mucosal samples were assessed. Sigmoid biopsies were collected post-intervention from subgroups for Ussing chamber experiments and gene transcription of barrier-related genes. Pectin intervention did not a ect in vivo gastroduodenal, small intestinal, colonic, and whole gut permeability in young adults nor in elderly (p ≥ 0.130). Salivary and fecal sIgA and serum IgA were not significantly di erent between pectin versus placebo in both age groups (p ≥ 0.128). In both young adults and elderly, no di erences in transepithelial electrical resistance and fluorescein flux (p ≥ 0.164) and relative expression of genes analyzed (p ≥ 0.222) were found between pectin versus placebo. In conclusion, intestinal barrier function was not a ected by four weeks pectin supplementation neither in healthy young adults nor in healthy elderly.

    A policy mixes approach to conceptualizing and measuring climate change adaptation policy
    Lesnikowski, Alexandra ; Ford, James D. ; Biesbroek, Robbert ; Berrang-Ford, Lea - \ 2019
    Climatic Change 156 (2019)4. - ISSN 0165-0009 - p. 447 - 469.

    Comparative research on climate change adaptation policy struggles with robust conceptualization and measurement of adaptation policy. Using a policy mixes approach to address this challenge, we characterize adaptation policy based on a general model of how governments govern issues of societal interest. We argue that this approach allows for context-sensitive measurement of adaptation policy, while being both comparable and parsimonious. This approach is tested in a study of adaptation policies adopted by 125 local governments located in Canada, France, Germany, the Netherlands, and the UK. Using a systematic data collection protocol, a total of 3328 adaptation policies were identified from local council archives between the periods of January 2010 and May 2017. Results of this analysis suggest that there is structured variation emerging in how local governments govern climate change adaptation, which justifies calls for comparative adaptation research to use measurements that capture the totality of adaptation policies being adopted by governments rather than focusing on specific types of adaptation policy. We conclude with a discussion of key issues for further developing of this approach.

    Structural Plasticity of Intrinsically Disordered LEA Proteins from Xerophyta schlechteri Provides Protection In Vitro and In Vivo
    Silva Artur, Mariana A. ; Rienstra, Juriaan ; Dennis, Timothy J. ; Farrant, Jill M. ; Ligterink, Wilco ; Hilhorst, Henk - \ 2019
    Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
    intrinsic disorder - late embryogenesis abundant proteins - plant desiccation tolerance - resurrection plants - Xerophyta

    Late embryogenesis abundant (LEA) proteins are essential to the ability of resurrection plants and orthodox seeds to protect the subcellular milieu against irreversible damage associated with desiccation. In this work, we investigated the structure and function of six LEA proteins expressed during desiccation in the monocot resurrection species Xerophyta schlechteri (XsLEAs). In silico analyses suggested that XsLEAs are hydrophilic proteins with variable intrinsically disordered protein (IDP) properties. Circular dichroism (CD) analysis indicated that these proteins are mostly unstructured in water but acquire secondary structure in hydrophobic solution, suggesting that structural dynamics may play a role in their function in the subcellular environment. The protective property of XsLEAs was demonstrated by their ability to preserve the activity of the enzyme lactate dehydrogenase (LDH) against desiccation, heat and oxidative stress, as well as growth of Escherichia coli upon exposure to osmotic and salt stress. Subcellular localization analysis indicated that XsLEA recombinant proteins are differentially distributed in the cytoplasm, membranes and nucleus of Nicotiana benthamiana leaves. Interestingly, a LEA_1 family protein (XsLEA1-8), showing the highest disorder-to-order propensity and protective ability in vitro and in vivo, was also able to enhance salt and drought stress tolerance in Arabidopsis thaliana. Together, our results suggest that the structural plasticity of XsLEAs is essential for their protective activity to avoid damage of various subcellular components caused by water deficit stress. XsLEA1-8 constitutes a potential model protein for engineering structural stability in vitro and improvement of water-deficit stress tolerance in plants.

    Tracking global climate change adaptation among governments
    Berrang-Ford, Lea ; Biesbroek, Robbert ; Ford, James D. ; Lesnikowski, Alexandra ; Tanabe, Andrew ; Wang, Frances M. ; Chen, Chen ; Hsu, Angel ; Hellmann, Jessica J. ; Pringle, Patrick ; Grecequet, Martina ; Amado, J.C. ; Huq, Saleemul ; Lwasa, Shuaib ; Heymann, S.J. - \ 2019
    Nature Climate Change 9 (2019)6. - ISSN 1758-678X - p. 440 - 449.

    The Paris Agreement and Katowice Climate Package articulate a clear mandate for all parties to undertake and document adaptation progress. Yet persistent challenges have prevented substantive developments in tracking adaptation and the assessment of adaptation actions and their outcomes. Here, we provide an overview of the challenges of adaptation tracking and propose a comprehensive conceptual framework for assessing adaptation progress by governments that is scalable over time and across contexts. The framework addresses the core components of adaptation assessment (vulnerability, goals and targets, adaptation efforts, and adaptation results) and characterizes subcomponents focused on adaptation effort (leadership, organizations and policy). In particular, we highlight how critical insights can be uncovered by systematically tracking policy efforts over time, and discusses novel approaches to data collection.

    Frontiers in data analytics for adaptation research: Topic modeling
    Lesnikowski, Alexandra ; Belfer, Ella ; Rodman, Emma ; Smith, Julie ; Biesbroek, Robbert ; Wilkerson, John D. ; Ford, James D. ; Berrang-Ford, Lea - \ 2019
    Wiley Interdisciplinary Reviews: Climate Change 10 (2019)3. - ISSN 1757-7780
    climate change adaptation - governance - policy - quantitative text analysis - topic models

    Rapid growth over the past two decades in digitized textual information represents untapped potential for methodological innovations in the adaptation governance literature that draw on machine learning approaches already being applied in other areas of computational social sciences. This Focus Article explores the potential for text mining techniques, specifically topic modeling, to leverage this data for large-scale analysis of the content of adaptation policy documents. We provide an overview of the assumptions and procedures that underlie the use of topic modeling, and discuss key areas in the adaptation governance literature where topic modeling could provide valuable insights. We demonstrate the diversity of potential applications for topic modeling with two examples that examine: (a) how adaptation is being talked about by political leaders in United Nations Framework Convention on Climate Change; and (b) how adaptation is being discussed by decision-makers and public administrators in Canadian municipalities using documents collected from 25 city council archives. This article is categorized under: Vulnerability and Adaptation to Climate Change > Institutions for Adaptation.

    Dissecting the genomic diversification of Late Embryogenesis Abundant (LEA) protein gene families in plants
    Silva Artur, M.A. ; Zhao, T. ; Ligterink, W. ; Schranz, Eric ; Hilhorst, H.W.M. - \ 2019
    Genome Biology 11 (2019)2. - ISSN 1474-7596 - p. 459 - 471.
    Late Embryogenesis Abundant (LEA) proteins include eight multi-gene families that are expressed in response to water loss during seed maturation and in vegetative tissues of desiccation tolerant species. To elucidate LEA proteins evolution and diversification, we performed a comprehensive synteny and phylogenetic analyses of the eight gene families across 60 complete plant genomes. Our integrated comparative genomic approach revealed that synteny conservation and diversification contributed to LEA family expansion and functional diversification in plants. We provide examples that: 1) the genomic diversification of the Dehydrin family contributed to differential evolution of amino acid sequences, protein biochemical properties, and gene expression patterns, and led to the appearance of a novel functional motif in angiosperms; 2) ancient genomic diversification contributed to the evolution of distinct intrinsically disordered regions of LEA_1 proteins; 3) recurrent tandem-duplications contributed to the large expansion of LEA_2; and, 4) dynamic synteny diversification played a role on the evolution of LEA_4 and its function on plant desiccation tolerance. Taken together, these results show that multiple evolutionary mechanisms have not only led to genomic diversification, but also to structural and functional plasticity among LEA proteins which have jointly contributed to the adaptation of plants to water-limiting environments.
    Straightforward Regeneration of Reduced Flavin Adenine Dinucleotide Required for Enzymatic Tryptophan Halogenation
    Ismail, Mohamed ; Schroeder, Lea ; Frese, Marcel ; Kottke, Tilman ; Hollmann, Frank ; Paul, Caroline E. ; Sewald, Norbert - \ 2019
    ACS Catalysis 9 (2019)2. - ISSN 2155-5435 - p. 1389 - 1395.
    enzymatic cofactor regeneration - FADH - flavin-dependent halogenases - hydride transfer - NADH mimics - regioselective chlorination

    Flavin-dependent halogenases are known to regioselectively introduce halide substituents into aromatic moieties, for example, the indole ring of tryptophan. The process requires halide salts and oxygen instead of molecular halogen in the chemical halogenation. However, the reduced cofactor flavin adenine dinucleotide (FADH2) has to be regenerated using a flavin reductase. Consequently, coupled biocatalytic steps are usually applied for cofactor regeneration. Nicotinamide adenine dinucleotide (NADH) mimics can be employed stoichiometrically to replace enzymatic cofactor regeneration in biocatalytic halogenation. Chlorination of l-tryptophan is successfully performed using such NADH mimics. The efficiency of this approach has been compared to the previously established enzymatic regeneration system using the two auxiliary enzymes flavin reductase (PrnF) and alcohol dehydrogenase (ADH). The reaction rates of some of the tested mimics were found to exceed that of the enzymatic system. Continuous enzymatic halogenation reaction for reaction scale-up is also possible.

    Enabling local public health adaptation to climate change
    Austin, Stephanie E. ; Ford, James D. ; Berrang-Ford, Lea ; Biesbroek, Robbert ; Ross, Nancy A. - \ 2019
    Social Science and Medicine 220 (2019). - ISSN 0277-9536 - p. 236 - 244.
    Adaptation - Adaptive capacity - Canada - Climate change - Germany - Health policy - Multi-level governance - Public health

    Local public health authorities often lack the capacity to adapt to climate change, despite being on the ‘front lines’ of climate impacts. Upper-level governments are well positioned to create an enabling environment for adaptation and build local public health authorities' capacity, yet adaptation literature has not specified how upper-level governments can build local-level adaptive capacity. In this paper we examine how federal and regional governments can contribute to enabling and supporting public health adaptation to climate change at the local level in federal systems. We outline the local level's self-assessed adaptive capacity for public health adaptation in Canadian and German comparative case studies, in terms of funding, knowledge and skills, organizations, and prioritization, drawing upon 30 semi-structured interviews. Based on interviewees' recommendations and complemented by scientific literature, we develop a set of practical measures that could enable or support local-level public health adaptation. We find that adaptive capacity varies widely between local public health authorities, but most report having insufficient funding and staff for adaptation activities. We propose 10 specific measures upper-level governments can take to build local public health authorities' capacity for adaptation, under the interrelated target areas of: building financial capital; developing and disseminating usable knowledge; collaborating and coordinating for shared knowledge; and claiming leadership. Federal and regional governments have an important role to play in enabling local-level public health adaptation, and have many instruments available to them to fulfill that role. Selecting and implementing measures to enable local public health authorities' adaptive capacity will require tailoring to, and consideration, of the local context and needs.

    Unfolding plant desiccation tolerance : evolution, structure, and function of LEA proteins
    Silva Artur, Mariana Aline - \ 2019
    Wageningen University. Promotor(en): H.W.M. Hilhorst, co-promotor(en): J.W. Ligterink. - Wageningen : Wageningen University - ISBN 9789463433860 - 174

    When plants colonized land they developed a wide range of adaptations to cope with life in a drier environment. One key adaptation was desiccation tolerance (DT) which is the ability to survive the removal of almost all cellular water without irreparable damage. DT is recurrent in orthodox seeds and in the vegetative body of species commonly known as ‘resurrection plants’. In this thesis a multilevel approach, combining genomics, transcriptomics, gene family evolution, protein structural and functional analysis, and seed physiology was employed in order to tackle curiosity-driven fundamental questions about the major mechanisms governing DT. Several mechanisms were found to be important for DT, including the coordinated activation of cell protection through Late Embryogenesis Abundant (LEA) proteins, which were shown to be common amongst resurrection plants and orthodox seeds. These findings aid to the comprehension of the complexity of DT in plants, and may provide transferrable knowledge to design more water-stress tolerant crops.

    When food systems meet sustainability – Current narratives and implications for actions
    Béné, Christophe ; Oosterveer, Peter ; Lamotte, Lea ; Brouwer, Inge D. ; Haan, Stef de; Prager, Steve D. ; Talsma, Elise F. ; Khoury, Colin K. - \ 2019
    World Development 113 (2019). - ISSN 0305-750X - p. 116 - 130.
    Discourse analysis - Food security and nutrition - Food systems - Healthy diet - Sustainability

    The concept of food system has gained prominence in recent years amongst both scholars and policy-makers. Experts from diverse disciplines and backgrounds have in particular discussed the nature and origin of the “unsustainability” of our modern food systems. These efforts tend, however, to be framed within distinctive disciplinary narratives. In this paper we propose to explore these narratives and to shed light on the explicit -or implicit- epistemological assumptions, mental models, and disciplinary paradigms that underpin those. The analysis indicates that different views and interpretations prevail amongst experts about the nature of the “crisis”, and consequently about the research and priorities needed to “fix” the problem. We then explore how sustainability is included in these different narratives and the link to the question of healthy diets. The analysis reveals that the concept of sustainability, although widely used by all the different communities of practice, remains poorly defined, and applied in different ways and usually based on a relatively narrow interpretation. In so doing we argue that current attempts to equate or subsume healthy diets within sustainability in the context of food system may be misleading and need to be challenged. We stress that trade-offs between different dimensions of food system sustainability are unavoidable and need to be navigated in an explicit manner when developing or implementing sustainable food system initiatives. Building on this overall analysis, a framework structured around several entry points including outcomes, core activities, trade-offs and feedbacks is then proposed, which allows to identify key elements necessary to support the transition toward sustainable food systems.

    Survey of subtidal anthropogenic marine debris (AMD) in Mayo Bay, Mati City, davao oriental, Philippines
    Abreo, Neil Angelo S. ; Macusi, Edison D. ; Jimenez, Lea A. - \ 2018
    The Philippine Journal of Crop Science 147 (2018)4. - ISSN 0031-7683 - p. 597 - 600.
    AMD - Marine debris - Mayo Bay - Philippines - Solid waste management

    Anthropogenic marine debris (AMD) is considered a global threat to the marine environment. Mortality from ingestion or entanglement in AMD is widely reported from marine animals and has harmful impacts on seagrass and corals. The distribution of AMD plays a vital role in its interaction with marine organisms. However, there is little information on AMD distribution in the Philippines – a country ranked as the third most significant contributor of AMD in the ocean. During the monitoring of dugong (Dugong dugon) feeding trails in Mati City, Davao Oriental, Philippines, AMD was recorded at one of the sites surveyed. Plastic debris was the most dominant in number and weight of total AMD collected. Here we present the first quantification, characterization, and distribution of AMD in a shallow subtidal area in Mati City, Philippines. More studies are needed to assess the impacts of AMD on the marine environment and organisms, particularly within the Philippines.

    Kauniolide synthase is a P450 with unusual hydroxylation and cyclization-elimination activity
    Liu, Qing ; Beyraghdar Kashkooli, Arman ; Manzano, David ; Pateraki, Irini ; Richard, Lea ; Kolkman, Pim ; Lucas, Maria Fátima ; Guallar, Victor ; Vos, Ric C.H. de; Franssen, Maurice C.R. ; Krol, Alexander van der; Bouwmeester, Harro - \ 2018
    Nature Communications 9 (2018)1. - ISSN 2041-1723

    Guaianolides are an important class of sesquiterpene lactones with unique biological and pharmaceutical properties. They have been postulated to be derived from germacranolides, but for years no progress has been made in the elucidation of their biosynthesis that requires an unknown cyclization mechanism. Here we demonstrate the isolation and characterization of a cytochrome P450 from feverfew (Tanacetum parthenium), kauniolide synthase. Kauniolide synthase catalyses the formation of the guaianolide kauniolide from the germacranolide substrate costunolide. Unlike most cytochrome P450s, kauniolide synthase combines stereoselective hydroxylation of costunolide at the C3 position, with water elimination, cyclization and regioselective deprotonation. This unique mechanism of action is supported by in silico modelling and docking experiments. The full kauniolide biosynthesis pathway is reconstructed in the heterologous hosts Nicotiana benthamiana and yeast, paving the way for biotechnological production of guaianolide-type sesquiterpene lactones.

    Do Administrative Traditions Matter for Climate Change Adaptation Policy? A Comparative Analysis of 32 High-Income Countries
    Biesbroek, Robbert ; Lesnikowski, Alexandra ; Ford, James D. ; Berrang-Ford, Lea ; Vink, Martinus - \ 2018
    Review of Policy Research 35 (2018)6. - ISSN 1541-132X - p. 881 - 906.
    administrative traditions - climate change adaptation - governance - policy innovation - public bureaucracy

    Although governments are developing and implementing policies to adapt to the impacts of climate change, it remains unclear which factors shape how states are developing these policies. This paper aims to assess whether or not administrative traditions matter for the formation of national climate change adaptation policy in 32 high-income countries. We operationalize administrative traditions based on five structural criteria: vertical dispersion of authority, horizontal coordination, interest mediation between state-society, role of public administrator, and how ideas enter bureaucracy. We construct a unique adaptation policy dataset that includes 32 high-income countries to test seven hypotheses. Our results indicate that countries’ adaptation policies align to some extent with their administrative structure, particularly dispersion of authority and horizontal coordination. However, we find limited evidence that other public bureaucracy factors are related to national adaptation policy. We conclude that administrative traditions matter, but that their influence should not be overestimated.

    Synteny-based phylogenomic networks for comparative genomics
    Zhao, Tao - \ 2018
    Wageningen University. Promotor(en): E. Schranz. - Wageningen : Wageningen University - ISBN 9789463433204 - 139

    For comparative genomics, relative gene orders or synteny holds key information to assess genomic innovations such as gene duplications, gene loss, or transpositions. While the number of reference genomes is growing exponentially, a major challenge is how to detect, represent, and visualize synteny relations of any genes of interest effectively across a large number of genomes.

    In this thesis, I present six chapters centering on a network approach for large-scale phylogenomic synteny analysis, and discuss how such a network approach can enhance our understanding of the evolutionary history of genes and genomes across broad phylogenetic groups and divergence times.

    In Chapter 1, I stress that synteny information is becoming more important at this genomics age with rapidly developing DNA sequencing technologies. It provides us another layer of data besides merely sequences, and could potentially be better used to improve phylogeny. I also summarized current available tools and gave an example of popular websites for synteny detection.

    In Chapter 2, I propose an outline performing synteny network analysis, which is based on three primary steps: pairwise whole genome comparisons, syntenic block detection and data fusion, and network visualization. Then with comparison to a previous synteny comparison result which use traditional parallel coordinate plots, I show that the network approach could present us a much clear, strong, and systematic graph, with integrated synteny information from 101 broadly distributed species.

    In Chapter 3, we analyzed synteny networks of the entire MADS-box transcription factor gene family from fifty-one completed plant genomes. We applied a k-cliques percolation method to cluster the synteny network. We found lineage-specific clusters that derive from transposition events for the regulators of floral development (APETALA3 and PI) and flowering-time (FLC) in the Brassicales and for the regulators of root-development (AGL17) in Poales. We also visualized big difference of synteny properties between Type I MADS-box genes and Type II MADS-box genes. We identified two large gene clusters that jointly encompass many key phenotypic regulatory Type II MADS-box gene clades (SEP1, SQUA, TM8, SEP3, FLC, AGL6 and TM3). This allows for a better understanding of how evolution has acted on a key regulatory gene family in the plant kingdom.

    In Chapter 4, we performed synteny network analysis of LEA gene families, which includes eight different subfamilies (LEA_1 to LEA_6, SMP, and DHN) and has a relatively chaotic classification. Synteny clusters provide us better pictures of genomic innovations and function diversification. For example recurrent tandem duplications contributed to LEA_2 family expansion, whereas synteny and protein sequence were highly conserved during the evolution of LEA_5.

    In Chapter 5, instead of the analysis of a particular gene family, I scale up the analysis to all the genes from all available genomes across kingdoms over significant evolutionary timescales. We used available genomes of 87 mammals and 107 flowering plants. We first compare synteny percentage with popular genome metrics such as BUSCO and N50, which reveal genomic architecture conservation and variation across kingdoms. We characterized and compare the properties of the whole network, using degree distribution and clustering results. Through phylogenomic profiling of size, degree and compositions of all clusters, we identified many phylogenomic genomic innovations (i.e. duplications, gene transpositions, gene loss), at the individual gene level, from tested mammal and angiosperm genomes.

    In Chapter 6, I summarize the merits of taking a network-based approach for synteny comparisons, and discuss current clustering methods for synteny data. I also mentioned several weakness, which could be further complemented in the future.

    Data, concepts and methods for large-n comparative climate change adaptation policy research : A systematic literature review
    Biesbroek, Robbert ; Berrang-Ford, Lea ; Ford, James D. ; Tanabe, Andrew ; Austin, Stephanie E. ; Lesnikowski, Alexandra - \ 2018
    Wiley Interdisciplinary Reviews: Climate Change 9 (2018)6. - ISSN 1757-7780
    Climate change adaptation - Comparative policy - Data collection - Methods - Systematic review

    Climate change adaptation research is dominated by in-depth, qualitative, single- or small-n case studies that have resulted in rich and in-depth understanding on adaptation processes and decision making in specific locations. Recently, the number of comparative adaptation policy cases has increased, focusing on examining, describing, and/or explaining how countries, regions, and vulnerable groups are adapting across a larger sample of contexts and over time. There are, however, critical empirical, conceptual and methodological choices and challenges for comparative adaptation research. This article systematically captures and assesses the current state of larger-n (n≥20 cases) comparative adaptation policy literature. We systematically analyze 72 peer-reviewed articles to identify the key choices and challenges authors face when conducting their research. We find among others that almost all studies use nonprobability sampling methods, few existing comparative adaptation datasets exist, most studies use easy accessible data which might not be most appropriate for the research question, many struggle to disentangle rhetoric from reality in adaptation, and very few studies engage in critical reflection of their conceptual, data and methodological choices and the implications for their findings. We conclude that efforts to increase data availability and use of more rigorous methodologies are necessary to advance comparative adaptation research. This article is categorized under: Vulnerability and Adaptation to Climate Change > Learning from Cases and Analogies

    Intergovernmental relations for public health adaptation to climate change in the federalist states of Canada and Germany
    Austin, Stephanie E. ; Ford, James D. ; Berrang-Ford, Lea ; Biesbroek, Robbert ; Tosun, Jale ; Ross, Nancy A. - \ 2018
    Global environmental change : human and policy dimensions 52 (2018). - ISSN 0959-3780 - p. 226 - 237.
    Canada - Climate change adaptation - Federalism - Germany - Intergovernmental relations - Public health

    Climate change is a significant threat to public health, and governments at all scales will need to adapt to protect the health of their populations. The impacts of climate change are highly localized and thus federal systems theoretically have the inherent advantage of allowing for regional diversity and policy experimentation in adaptation. However, there are also higher levels of conflict and stalemates in federal systems than in unitary systems, complicating intergovernmental relations and coordination necessary for public health adaptation. We examine how intergovernmental dynamics are patterned across national, regional and local levels of government for public health adaptation to climate change, drawing upon semi-structured interviews (n = 28) in comparative embedded case studies of Canada and Germany. We find that coordination between levels of government specifically for climate change and health is rare, but climate change issues are occasionally discussed through working groups or through existing methods of public health coordination. These findings have implications for national and regional governments in federal systems seeking to enable sub-national public health adaptation to climate change and create synergies between levels of government.

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