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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Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity
Schurink, Anouk ; Silva, Vinicius H. da; Velie, Brandon D. ; Dibbits, Bert W. ; Crooijmans, Richard P.M.A. ; François, Liesbeth ; Janssens, Steven ; Stinckens, Anneleen ; Blott, Sarah ; Buys, Nadine ; Lindgren, Gabriella ; Ducro, Bart J. - \ 2018
BMC Genetics 19 (2018)1. - ISSN 1471-2156
Copy number variations - Friesian horse - Genome-wide association study - Insect bite hypersensitivity

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results: Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.

Symmetric assembly and disassembly processes in an ecological network
Tylianakis, Jason M. ; Martínez-García, Laura B. ; Richardson, Sarah J. ; Peltzer, Duane A. ; Dickie, Ian A. - \ 2018
Ecology Letters 21 (2018)6. - ISSN 1461-023X - p. 896 - 904.
Community assembly - ecosystem development - mutualist network - mycorrhizal symbiosis - preferential attachment - retrogression - succession
The processes whereby ecological networks emerge, persist and decay throughout ecosystem development are largely unknown. Here we study networks of plant and arbuscular mycorrhizal fungal (AMF) communities along a 120 000 year soil chronosequence, as they undergo assembly (progression) and then disassembly (retrogression). We found that network assembly and disassembly were symmetrical, self-reinforcing processes that together were capable of generating key attributes of network architecture. Plant and AMF species that had short indirect paths to others in the community (i.e. high centrality), rather than many direct interaction partners (i.e. high degree), were best able to attract new interaction partners and, in the case of AMF species, also to retain existing interactions with plants during retrogression. We then show using simulations that these non-random patterns of attachment and detachment promote nestedness of the network. These results have implications for predicting extinction sequences, identifying focal points for invasions and suggesting trajectories for restoration.
Climate-smart land use requires local solutions, transdisciplinary research, policy coherence and transparency
Carter, Sarah ; Arts, Bas ; E. Giller, Ken ; Soto Golcher, Cinthia ; Kok, Kasper ; Koning, Jessica De; Noordwijk, Meine Van; Reidsma, Pytrik ; Rufino, Mariana C. ; Salvini, Giulia ; Verchot, Louis ; Wollenberg, Eva ; Herold, Martin - \ 2018
Carbon Management (2018). - ISSN 1758-3004 - 11 p.
Successfully meeting the mitigation and adaptation targets of the Paris Climate Agreement (PA) will depend on strengthening the ties between forests and agriculture. Climate-smart land use can be achieved by integrating climate-smart agriculture (CSA) and REDD+. The focus on agriculture for food security within a changing climate, and on forests for climate change mitigation and adaptation, can be achieved simultaneously with a transformational change in the land-use sector. Striving for both independently will lead to competition for land, inefficiencies in monitoring and conflicting agendas. Practical solutions exist for specific contexts that can lead to increased agricultural output and forest protection. Landscape-level emissions accounting can be used to identify these practices. Transdisciplinary research agendas can identify and prioritize solutions and targets for integrated mitigation and adaptation interventions. Policy coherence must be achieved at a number of levels, from international to local, to avoid conflicting incentives. Transparency must lastly be integrated, through collaborative design of projects, and open data and methods. Climate-smart land use requires all these elements, and will increase the likelihood of successful REDD+ and CSA interventions. This will support the PA as well as other initiatives as part of the Sustainable Development Goals.
Associations of omega-3 fatty acid supplement use with cardiovascular disease risks meta-analysis of 10 trials involving 77 917 individuals
Aung, Theingi ; Halsey, Jim ; Kromhout, Daan ; Gerstein, Hertzel C. ; Marchioli, Roberto ; Tavazzi, Luigi ; Geleijnse, Johanna M. ; Rauch, Bernhard ; Ness, Andrew ; Galan, Pilar ; Chew, Emily Y. ; Bosch, Jackie ; Collins, Rory ; Lewington, Sarah ; Armitage, Jane ; Clarke, Robert - \ 2018
JAMA Cardiology 3 (2018)3. - ISSN 2380-6583 - p. 225 - 234.
IMPORTANCE Current guidelines advocate the use of marine-derived omega-3 fatty acids supplements for the prevention of coronary heart disease and major vascular events in people with prior coronary heart disease, but large trials of omega-3 fatty acids have produced conflicting results. OBJECTIVE To conduct ameta-analysis of all large trials assessing the associations of omega-3 fatty acid supplements with the risk of fatal and nonfatal coronary heart disease and major vascular events in the full study population and prespecified subgroups. DATA SOURCES AND STUDY SELECTION This meta-analysis included randomized trials that involved at least 500 participants and a treatment duration of at least 1 year and that assessed associations of omega-3 fatty acids with the risk of vascular events. DATA EXTRACTION AND SYNTHESIS Aggregated study-level datawere obtained from 10 large randomized clinical trials. Rate ratios for each trial were synthesized using observed minus expected statistics and variances. Summary rate ratios were estimated by a fixed-effects meta-analysis using 95%confidence intervals for major diseases and 99%confidence intervals for all subgroups. MAIN OUTCOMES AND MEASURES The main outcomes included fatal coronary heart disease, nonfatalmyocardial infarction, stroke, major vascular events, and all-cause mortality, as well as major vascular events in study population subgroups. RESULTS Of the 77 917 high-risk individuals participating in the 10 trials, 47 803 (61.4%) were men, and the mean age at entry was 64.0 years; the trials lasted a mean of 4.4 years. The associations of treatment with outcomes were assessed on 6273 coronary heart disease events (2695 coronary heart disease deaths and 2276 nonfatalmyocardial infarctions) and 12 001 major vascular events. Randomization to omega-3 fatty acid supplementation (eicosapentaenoic acid dose range, 226-1800mg/d) had no significant associations with coronary heart disease death (rate ratio [RR], 0.93; 99%CI, 0.83-1.03; P = .05), nonfatal myocardial infarction (RR, 0.97; 99%CI, 0.87-1.08; P = .43) or any coronary heart disease events (RR, 0.96; 95%CI, 0.90-1.01; P = .12). Neither did randomization to omega-3 fatty acid supplementation have any significant associations with major vascular events (RR, 0.97; 95% CI, 0.93-1.01; P = .10), overall or in any subgroups, including subgroups composed of persons with prior coronary heart disease, diabetes, lipid levels greater than a given cutoff level, or statin use. CONCLUSIONS AND RELEVANCE This meta-analysis demonstrated that omega-3 fatty acids had no significant association with fatal or nonfatal coronary heart disease or any major vascular events. It provides no support for current recommendations for the use of such supplements in people with a history of coronary heart disease.
Interregional flows of ecosystem services : Concepts, typology and four cases
Schröter, Matthias ; Koellner, Thomas ; Alkemade, Rob ; Arnhold, Sebastian ; Bagstad, Kenneth J. ; Erb, Karl Heinz ; Frank, Karin ; Kastner, Thomas ; Kissinger, Meidad ; Liu, Jianguo ; López-Hoffman, Laura ; Maes, Joachim ; Marques, Alexandra ; Martín-López, Berta ; Meyer, Carsten ; Schulp, Catharina J.E. ; Thober, Jule ; Wolff, Sarah ; Bonn, Aletta - \ 2018
Ecosystem Services 31 (2018). - ISSN 2212-0416 - p. 231 - 241.
Drivers - Effects - Spatial flows - Sustainability - Teleconnection - Telecoupling
Conserving and managing global natural capital requires an understanding of the complexity of flows of ecosystem services across geographic boundaries. Failing to understand and to incorporate these flows into national and international ecosystem assessments leads to incomplete and potentially skewed conclusions, impairing society's ability to identify sustainable management and policy choices. In this paper, we synthesise existing knowledge and develop a conceptual framework for analysing interregional ecosystem service flows. We synthesise the types of such flows, the characteristics of sending and receiving socio-ecological systems, and the impacts of ecosystem service flows on interregional sustainability. Using four cases (trade of certified coffee, migration of northern pintails, flood protection in the Danube watershed, and information on giant pandas), we test the conceptual framework and show how an enhanced understanding of interregional telecouplings in socio-ecological systems can inform ecosystem service-based decision making and governance with respect to sustainability goals.
Optimising cost-effectiveness of freedom from disease surveillance-Bluetongue Virus Serotype 8 as an example
Rüegg, Simon R. ; Welby, Sarah ; Yassin, Hurria ; Stede, Yves Van der; Nafzger, Rebekka ; Saatkamp, Helmut ; Schüpbach-Regula, Gertraud ; Stärk, Katharina D.C. - \ 2018
Preventive Veterinary Medicine (2018). - ISSN 0167-5877
Bluetongue virus serotype 8 - Cost-effectiveness analysis - Cost-effectiveness optimisation - Disease surveillance - Risk-based surveillance - Scenario tree modelling
The aim of this study was to propose a procedure for optimising the cost-effectiveness of vector borne disease surveillance using a scenario tree model and cost-effectiveness analysis. The surveillance systems for Bluetongue Virus serotype 8 (BTV-8) implemented in Switzerland and Belgium were used as examples. In twenty four different, simulated population structures, passive surveillance and five designs of active surveillance were investigated. The influence of surveillance system design and parameters such as farmer disease awareness, veterinary disease awareness, herd and within-herd design prevalence on the overall surveillance system sensitivity were assessed. Furthermore, the cost-effectiveness of mandatory and voluntary vaccination regimes in relation to disease surveillance was investigated.Under the assumption that BTV-8 manifests clinically, freedom from disease in a population can be established with almost certainty over the period of one year using clinical surveillance alone. Additional investment in active surveillance would therefore economically only be justified, if no clinical manifestation is suspected or other surveillance objectives are to be provided such as early detection. The best cost-effectiveness is obtained by sampling more herds rather than more animals within a herd. Mandatory vaccination reduces the cost of surveillance by 0.26 € per vaccine and voluntary vaccination only marginally reduces the cost of risk-based surveillance, by reducing the population at risk. Finally, in populations with predominantly dairy cattle, bulk-tank milk testing is the method of choice to actively demonstrate freedom from disease.
Economic impacts of marine ecological change : Review and recent contributions of the VECTORS project on European marine waters
Groeneveld, Rolf A. ; Bartelings, Heleen ; Börger, Tobias ; Bosello, Francesco ; Buisman, Erik ; Delpiazzo, Elisa ; Eboli, Fabio ; Fernandes, Jose A. ; Hamon, Katell G. ; Hattam, Caroline ; Loureiro, Maria ; Nunes, Paulo A.L.D. ; Piwowarczyk, Joanna ; Schasfoort, Femke E. ; Simons, Sarah L. ; Walker, Adam N. - \ 2018
Estuarine Coastal and Shelf Science 201 (2018). - ISSN 0272-7714 - p. 152 - 163.
Algal blooms - Climatic changes - Economic analysis - Fisheries - Introduced species - Recreation
Marine ecological change is likely to have serious potential economic consequences for coastal economies all over the world. This article reviews the current literature on the economic impacts of marine ecological change, as well as a number of recent contributions to this literature carried out under the VECTORS project. We focus on three main types of change, namely invasive alien species; outbreak-forming species, such as jellyfish and toxic algae; and gradual changes in species distribution and productivity. The case studies available in the literature demonstrate that the impacts of invasions and outbreaks on fisheries, aquaculture, and tourism can potentially amount to several tens of millions of dollars each year in some regions. Moreover, stated preference studies suggest a substantial impact on coastal tourism and non-use values that is likely not visible in case studies of specific outbreak events. Climate-driven gradual changes in distribution and productivity of commercial fish stocks will have an impact on fisheries, although these impacts are likely to be overshadowed by much larger changes in prices of seafood and fuel.
Fusarium metavorans sp. Nov. : The frequent opportunist â € FSSC6'
Al-Hatmi, Abdullah M.S. ; Ahmed, Sarah A. ; Diepeningen, Anne D. Van; Drogari-Apiranthitou, Miranda ; Verweij, Paul E. ; Meis, Jacques F. ; Hoog, G.S. De - \ 2018
Medical mycology 56 (2018). - ISSN 1369-3786 - p. S144 - S152.
fusariosis - Fusarium metavorans - molecular phylogenetics - morphology - RPB2 - taxonomy - TEF1
The Fusarium solani species complex (FSSC) is the most common group of fusaria associated with superficial and life-threatening infections in humans. Here we formally introduce Fusarium metavorans sp. Nov., widely known as FSSC6 (Fusarium solani species complex lineage 6), one of the most frequent agents of human opportunistic infections. The species is described with multilocus molecular data including sequences of internal transcribed spacer region (ITS), portions of the translation elongation factor 1-a gene (TEF1), and the partial RNA polymerase II gene (rPB2). A phylogenetic approach was used to evaluate species delimitation. Topologies of the trees were concordant. Phylogenetic analyses suggest that the FSSC consists of three major clades encompassing a large number of phylogenetic species; Fusarium metavorans corresponds to phylogenetic species 6 within FSSC clade 3. The species has a global distribution and a wide ecological amplitude, also including strains from soil and agents of opportunistic plant disease; it was also isolated from the gut of the wood-boring cerambycid beetle Anoplophora glabripennis.
A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
Recognition of microbial viability via TLR8 drives TFH cell differentiation and vaccine responses
Ugolini, Matteo ; Gerhard, Jenny ; Burkert, Sanne ; Jensen, Kristoffer Jarlov ; Georg, Philipp ; Ebner, Friederike ; Volkers, Sarah M. ; Thada, Shruthi ; Dietert, Kristina ; Bauer, Laura ; Schäfer, Alexander ; Helbig, Elisa T. ; Opitz, Bastian ; Kurth, Florian ; Sur, Saubashya ; Dittrich, Nickel ; Gaddam, Sumanlatha ; Conrad, Melanie L. ; Benn, Christine S. ; Blohm, Ulrike ; Gruber, Achim D. ; Hutloff, Andreas ; Hartmann, Susanne ; Boekschoten, Mark V. ; Müller, Michael ; Jungersen, Gregers ; Schumann, Ralf R. ; Suttorp, Norbert ; Sander, Leif E. - \ 2018
Nature Reviews. Immunology 19 (2018)4. - ISSN 1529-2908 - p. 386 - 396.
Live attenuated vaccines are generally highly efficacious and often superior to inactivated vaccines, yet the underlying mechanisms of this remain largely unclear. Here we identify recognition of microbial viability as a potent stimulus for follicular helper T cell (TFH cell) differentiation and vaccine responses. Antigen-presenting cells (APCs) distinguished viable bacteria from dead bacteria through Toll-like receptor 8 (TLR8)-dependent detection of bacterial RNA. In contrast to dead bacteria and other TLR ligands, live bacteria, bacterial RNA and synthetic TLR8 agonists induced a specific cytokine profile in human and porcine APCs, thereby promoting TFH cell differentiation. In domestic pigs, immunization with a live bacterial vaccine induced robust TFH cell and antibody responses, but immunization with its heat-killed counterpart did not. Finally, a hypermorphic TLR8 polymorphism was associated with protective immunity elicited by vaccination with bacillus Calmette-Guérin (BCG) in a human cohort. We have thus identified TLR8 as an important driver of TFH cell differentiation and a promising target for TFH cell-skewing vaccine adjuvants.
Mutation of adjacent cysteine residues in the NSs protein of Rift Valley fever virus results in loss of virulence in mice
Monteiro, Gaby E.R. ; Jansen van Vuren, Petrus ; Wichgers Schreur, Paul J. ; Odendaal, Lieza ; Clift, Sarah J. ; Kortekaas, Jeroen ; Paweska, Janusz T. - \ 2018
Virus Research 249 (2018). - ISSN 0168-1702 - p. 31 - 44.
Attenuation - Cysteine - Mutations - NSs protein - Rift Valley fever virus - Virulence
The NSs protein encoded by the S segment of Rift Valley fever virus (RVFV) is the major virulence factor, counteracting the host innate antiviral defence. It contains five highly conserved cysteine residues at positions 39, 40, 149, 178 and 194, which are thought to stabilize the tertiary and quaternary structure of the protein. Here, we report significant differences between clinical, virological, histopathological and host gene responses in BALB/c mice infected with wild-type RVFV (wtRVFV) or a genetic mutant having a double cysteine-to-serine substitution at residues 39 and 40 of the NSs protein (RVFV-C39S/C40S). Mice infected with the wtRVFV developed a fatal acute disease; characterized by high levels of viral replication, severe hepatocellular necrosis, and massive up-regulation of transcription of genes encoding type I and −II interferons (IFN) as well as pro-apoptotic and pro-inflammatory cytokines. The RVFV-C39S/C40S mutant did not cause clinical disease and its attenuated virulence was consistent with virological, histopathological and host gene expression findings in BALB/c mice. Clinical signs in mice infected with viruses containing cysteine-to-serine substitutions at positions 178 or 194 were similar to those occurring in mice infected with the wtRVFV, while a mutant containing a substitution at position 149 caused mild, non-fatal disease in mice. As mutant RVFV-C39S/C40S showed an attenuated phenotype in mice, the molecular mechanisms behind this attenuation were further investigated. The results show that two mechanisms are responsible for the attenuation; (1) loss of the IFN antagonistic propriety characteristic of the wtRVFV NSs and (2) the inability of the attenuated mutant to degrade Proteine Kinase R (PKR).
Deforestation and agriculture in the tropics: carbon emissions and options for mitigation
Carter, Sarah - \ 2018
University. Promotor(en): Martin Herold; Lammert Kooistra, co-promotor(en): L. Verchot. - Wageningen : Wageningen University - ISBN 9789463438322 - 164

Agriculture is the largest driver of deforestation globally, and this conversion of land from forests to agriculture, results in emissions which are contributing to climate change. This thesis focuses on exploring agriculture-driven deforestation at the country level, from the perspective of quantifying emissions, estimating the potential for mitigation, including identifying potential barriers to success, and highlighting enabling conditions for mitigation of these emissions. Efforts to reduce deforestation are being undertaken, for example through the mechanism REDD+; reducing emissions from deforestation and forest degradation and the role of conservation, sustainable management of forests and enhancement of forest carbon stocks in developing countries. At the same time, efforts are underway to try to reduce hunger by increasing food security (for example through the sustainable development goals (SDGs)). Competition for land can result when both these goals are pursued at the same time, because forested land is protected for carbon storage, while agricultural land is expanded (often into forests) to provide sufficient land for growing food. There are several ways in which both goals, forest protection and food security might be achieved together, and we focus on assessing the potential of two approaches which can potentially spare forested land. These approaches are: increasing production on existing agricultural land, and expanding agriculture onto non-forested available land. Emerging phenomena such as Large Scale Land Acquisitions (LSLA, otherwise known as land grabs) add to the complexity of the challenge, and we discuss the potential threat which LSLA has on forested land, and how to avoid LSLA for agriculture in forested land. A transformational change of the land sector is proposed to ensure that both goals can be met. Several ingredients are required to achieve a transformational change, and linking REDD+ to Climate Smart Agriculture (CSA) approaches is discussed. CSA interventions are those which are able to reduce emissions or store carbon while increasing the adaptive capacity of agriculture to climate change and increasing food production.

Chapter 2 provides new estimates of emissions from agriculture-driven deforestation in 91 countries using a data-driven approach. Latin America was found to have the highest emissions, and these emissions peaked between 2000 and 2005 and then declined. Emissions in Africa has been rising since 1990, with the countries in the Congo Basin being particular contributors to this rise in emissions. Uncertainties of these country emission estimates are ±62.4% (average for 1990-2015), and emissions from Asia are the most uncertain. The uncertainty of the input datasets was used to estimate the uncertainty of the emissions estimate, and the area of deforestation, and fraction which agriculture is driving deforestation were found to be the largest contributors to uncertainty of the emissions estimates. Increasing the certainty of these two data types should be a priority, and will lead to an increased certainty for the emissions estimates.

Chapter 3 compares direct and indirect emissions from agriculture at the national level, where direct are emissions from existing agricultural land, and indirect emissions are those from agriculture-driven deforestation. A decision tree was produced which can be used to guide decision making by identifying priority countries for mitigation initiatives. The decision tree uses several indicators related to the potential for mitigation, enabling environment, and associated risks to livelihoods to identify countries which have the most potential for the mitigation of either direct or indirect agricultural emissions. Six priority countries are highlighted as having a good mitigation potential for agriculture-driven deforestation while having a good enabling environment (in this case engagement in REDD+) and which also have low risks to livelihoods from the implementation of interventions in the agriculture sector. They are: Panama, Paraguay, Ecuador, Mexico, Malaysia and Peru.

Chapter 4 focusses on LSLA, and their potential impacts on forests. A country level analysis was carried out, and the characteristics which are typically found in countries which have LSLA were described. Countries which have these characteristics and which do not yet have LSLA are for example considered to be at risk from LSLA. Countries which have LSLA or are at risk from LSLA were assessed for the risk of LSLA-driven deforestation. Other key targets for interventions to reduce deforestation are highlighted, such as those countries with large numbers of LSLA and which already have a lot of agriculture-driven deforestation. The potential conflicts between LSLA and REDD+ are discussed, and investor-side policies such as zero deforestation pledges from commodity producers, green procurement policies, and initiatives such as the Roundtable For Sustainable Palm Oil are highlighted as potential solutions to these conflicts. Lessons learned from implementing REDD+, which has a number of shared characteristics with LSLA, can be applied in order to reduce the negative impacts of LSLA.

Chapter 5 discusses the potential for forest-land sparing interventions to be implemented in the agriculture sector. A transformative change which incorporates multiple interventions and brings together the forest and agriculture sectors is proposed. Climate Smart Agriculture approaches should be considered, but only when they do not lead to expansion of agriculture into forests. The need for supporting policies to avoid this occurring is discussed. Policy coherence is a barrier to this change as policies favouring both conversion to agriculture (including those which enable LSLA), and forest protection can occur in the same place. The use of the landscape approach as a platform to address this challenge is discussed. Landscape-level emissions accounting, which takes into consideration both direct and indirect emissions from agriculture, can be used to evaluate the impact of mitigation interventions across sectors. The need for transparency in the land sector, in relation to emissions reporting in particular is introduced, and is a key requirement for access to carbon finance which can potentially support forest land-sparing interventions.

Chapter 6 concludes the thesis, and discusses the wider implications for this work. The link between the findings in this thesis and the SDGs is explored. The SDGs may lead to future competition for land due to goals which focus on reducing hunger, protecting forests and increasing the proportion of renewable energy unless action is taken. Future data needs are discussed, as although we provide (in chapter 2) new data on agriculture-driven deforestation, they are still uncertain and data on potential future trends in agriculture-driven deforestation are not available. The need for consideration of emissions related to the impact of agriculture on forest degradation and on carbon losses in soils is another data gap, and relates to recent efforts to restore degraded land – which could be one of the most promising mitigation efforts which can also support the production of more food for growing global populations. The urgent need to address climate change highlights the opportunities in the land sector, not only to mitigate emissions, but also to promote food security.

Mycokey round table discussions of future directions in research on chemical detection methods, genetics and biodiversity of mycotoxins
Leslie, John F. ; Lattanzio, Veronica ; Audenaert, Kris ; Battilani, Paola ; Cary, Jeffrey ; Chulze, Sofia N. ; Saeger, Sarah De; Gerardino, Annamaria ; Karlovsky, Petr ; Liao, Yu Cai ; Maragos, Chris M. ; Meca, Giuseppe ; Medina, Angel ; Moretti, Antonio ; Munkvold, Gary ; Mulè, Giuseppina ; Njobeh, Patrick ; Pecorelli, Ivan ; Perrone, Giancarlo ; Pietri, Amedeo ; Palazzini, Juan M. ; Proctor, Robert H. ; Rahayu, Endang S. ; Ramírez, Maria L. ; Samson, Robert ; Stroka, Jörg ; Sulyok, Michael ; Sumarah, Mark ; Waalwijk, Cees ; Zhang, Qi ; Zhang, Hao ; Logrieco, Antonio F. - \ 2018
Toxins 10 (2018)3. - ISSN 2072-6651
Antibodies - Biological control - Communication with non-scientists - Metabolomics - Microbiome - Multi-mycotoxin detection protocols - Nominal group discussion technique - Proteomics - Transcriptomics
MycoKey, an EU-funded Horizon 2020 project, includes a series of “Roundtable Discussions” to gather information on trending research areas in the field of mycotoxicology. This paper includes summaries of the Roundtable Discussions on Chemical Detection and Monitoring of mycotoxins and on the role of genetics and biodiversity in mycotoxin production. Discussions were managed by using the nominal group discussion technique, which generates numerous ideas and provides a ranking for those identified as the most important. Four questions were posed for each research area, as well as two questions that were common to both discussions. Test kits, usually antibody based, were one major focus of the discussions at the Chemical Detection and Monitoring roundtable because of their many favorable features, e.g., cost, speed and ease of use. The second area of focus for this roundtable was multi-mycotoxin detection protocols and the challenges still to be met to enable these protocols to become methods of choice for regulated mycotoxins. For the genetic and biodiversity group, both the depth and the breadth of trending research areas were notable. For some areas, e.g., microbiome studies, the suggested research questions were primarily of a descriptive nature. In other areas, multiple experimental approaches, e.g., transcriptomics, proteomics, RNAi and gene deletions, are needed to understand the regulation of toxin production and mechanisms underlying successful biological controls. Answers to the research questions will provide starting points for developing acceptable prevention and remediation processes. Forging a partnership between scientists and appropriately-placed communications experts was recognized by both groups as an essential step to communicating risks, while retaining overall confidence in the safety of the food supply and the integrity of the food production chain.
Control of Lyme borreliosis and other Ixodes ricinus-borne diseases
Sprong, Hein ; Azagi, Tal ; Hoornstra, Dieuwertje ; Nijhof, Ard M. ; Knorr, Sarah ; Baarsma, M.E. ; Hovius, Joppe W. - \ 2018
Parasites & Vectors 11 (2018)1. - ISSN 1756-3305
Anaplasmosis - Ixodes ricinus - Lyme borreliosis - Prevention - Tick-borne encephalitis - Transmission cycles - Vaccines
Lyme borreliosis (LB) and other Ixodes ricinus-borne diseases (TBDs) are diseases that emerge from interactions of humans and domestic animals with infected ticks in nature. Nature, environmental and health policies at (inter)national and local levels affect the risk, disease burden and costs of TBDs. Knowledge on ticks, their pathogens and the diseases they cause have been increasing, and resulted in the discovery of a diversity of control options, which often are not highly effective on their own. Control strategies involving concerted actions from human and animal health sectors as well as from nature managers have not been formulated, let alone implemented. Control of TBDs asks for a "health in all policies" approach, both at the (inter)national level, but also at local levels. For example, wildlife protection and creating urban green spaces are important for animal and human well-being, but may increase the risk of TBDs. In contrast, culling or fencing out deer decreases the risk for TBDs under specific conditions, but may have adverse effects on biodiversity or may be societally unacceptable. Therefore, in the end, nature and health workers together must carry out tailor-made control options for the control of TBDs for humans and animals, with minimal effects on the environment. In that regard, multidisciplinary approaches in environmental, but also medical settings are needed. To facilitate this, communication and collaboration between experts from different fields, which may include patient representatives, should be promoted.
Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance
Kema, Gerrit H.J. ; Mirzadi Gohari, Amir ; Aouini, Lamia ; Gibriel, Hesham A.Y. ; Ware, Sarah B. ; Den Bosch, Frank van; Manning-Smith, Robbie ; Alonso-Chavez, Vasthi ; Helps, Joe ; M’Barek, Sarrah Ben; Mehrabi, Rahim ; Diaz-Trujillo, Caucasella ; Zamani, Elham ; Schouten, Henk J. ; Lee, Theo A.J. van der; Waalwijk, Cees ; Waard, Maarten A. de; Wit, Pierre J.G.M. de; Verstappen, Els C.P. ; Thomma, Bart P.H.J. ; Meijer, Harold J.G. ; Seidl, Michael F. - \ 2018
Nature Genetics 50 (2018). - ISSN 1061-4036 - p. 375 - 380.
Host resistance and fungicide treatments are cornerstones of plant-disease control. Here, we show that these treatments allow sex and modulate parenthood in the fungal wheat pathogen Zymoseptoria tritici. We demonstrate that the Z. tritici–wheat interaction complies with the gene-for-gene model by identifying the effector AvrStb6, which is recognized by the wheat resistance protein Stb6. Recognition triggers host resistance, thus implying removal of avirulent strains from pathogen populations. However, Z. tritici crosses on wheat show that sex occurs even with an avirulent parent, and avirulence alleles are thereby retained in subsequent populations. Crossing fungicide-sensitive and fungicide-resistant isolates under fungicide pressure results in a rapid increase in resistance-allele frequency. Isolates under selection always act as male donors, and thus disease control modulates parenthood. Modeling these observations for agricultural and natural environments reveals extended durability of host resistance and rapid emergence of fungicide resistance. Therefore, fungal sex has major implications for disease control.
Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels
Jiang, Xia ; O'Reilly, Paul F. ; Aschard, Hugues ; Hsu, Yi Hsiang ; Richards, J.B. ; Dupuis, Josée ; Ingelsson, Erik ; Karasik, David ; Pilz, Stefan ; Berry, Diane ; Kestenbaum, Bryan ; Zheng, Jusheng ; Luan, Jianan ; Sofianopoulou, Eleni ; Streeten, Elizabeth A. ; Albanes, Demetrius ; Lutsey, Pamela L. ; Yao, Lu ; Tang, Weihong ; Econs, Michael J. ; Wallaschofski, Henri ; Völzke, Henry ; Zhou, Ang ; Power, Chris ; McCarthy, Mark I. ; Michos, Erin D. ; Boerwinkle, Eric ; Weinstein, Stephanie J. ; Freedman, Neal D. ; Huang, Wen Yi ; Schoor, Natasja M. van; Velde, Nathalie van der; Groot, Lisette C.P.G.M. de; Enneman, Anke ; Cupples, L.A. ; Booth, Sarah L. ; Vasan, Ramachandran S. ; Liu, Ching Ti ; Zhou, Yanhua ; Ripatti, Samuli ; Ohlsson, Claes ; Vandenput, Liesbeth ; Lorentzon, Mattias ; Eriksson, Johan G. ; Shea, M.K. ; Houston, Denise K. ; Kritchevsky, Stephen B. ; Liu, Yongmei ; Lohman, Kurt K. ; Ferrucci, Luigi ; Peacock, Munro ; Gieger, Christian ; Beekman, Marian ; Slagboom, Eline ; Deelen, Joris ; Deelen, Joris ; Heemst, Diana van; Kleber, Marcus E. ; März, Winfried ; Boer, Ian H. De; Wood, Alexis C. ; Rotter, Jerome I. ; Rich, Stephen S. ; Robinson-Cohen, Cassianne ; Heijer, Martin Den; Jarvelin, Marjo Riitta ; Jarvelin, Marjo Riitta ; Cavadino, Alana ; Cavadino, Alana ; Joshi, Peter K. ; Wilson, James F. ; Hayward, Caroline ; Lind, Lars ; Michaëlsson, Karl ; Trompet, Stella ; Zillikens, M.C. ; Uitterlinden, Andre G. ; Rivadeneira, Fernando - \ 2018
Nature Communications 9 (2018)1. - ISSN 2041-1723
Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10 -9 at rs8018720 in SEC23A, and P = 1.9×10 -14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.
Agriculture-driven deforestation in the tropics from 1990 to-2015: emissions, trends and uncertainties
Carter, Sarah ; Herold, Martin ; Avitabile, Valerio ; Bruin, Sytze de; Sy, Veronique de; Kooistra, Lammert ; Rufino, Mariana C. - \ 2018
Environmental Research Letters 13 (2018)1. - ISSN 1748-9326
Limited data exists on emissions from agriculture-driven deforestation, and available data are typically uncertain. In this paper, we provide comparable estimates of emissions from both all deforestation and agriculture-driven deforestation, with uncertainties for 91 countries across the tropics between 1990 and 2015. Uncertainties associated with input datasets (activity data and emissions factors) were used to combine the datasets, where most certain datasets contribute the most. This method utilizes all the input data, while minimizing the uncertainty of the emissions estimate. The uncertainty of input datasets was influenced by the quality of the data, the sample size (for sample-based datasets), and the extent to which the timeframe of the data matches the period of interest. Area of deforestation, and the agriculture-driver factor (extent to which agriculture drives deforestation), were the most uncertain components of the emissions estimates, thus improvement in the uncertainties related to these estimates will provide the greatest reductions in uncertainties of emissions estimates. Over the period of the study, Latin America had the highest proportion of deforestation driven by agriculture (78%), and Africa had the lowest (62%). Latin America had the highest emissions from agriculture-driven deforestation, and these peaked at 974 ± 148 Mt CO2 yr−1 in 2000–2005. Africa saw a continuous increase in emissions between 1990 and 2015 (from 154 ± 21–412 ± 75 Mt CO2 yr−1), so mitigation initiatives could be prioritized there. Uncertainties for emissions from agriculture-driven deforestation are ± 62.4% (average over 1990–2015), and uncertainties were highest in Asia and lowest in Latin America. Uncertainty information is crucial for transparency when reporting, and gives credibility to related mitigation initiatives. We demonstrate that uncertainty data can also be useful when combining multiple open datasets, so we recommend new data providers to include this information.
Surveying selected European feed and livestock production chains for features enabling the case-specific post-market monitoring of livestock for intake and potential health impacts of animal feeds derived from genetically modified crops
Kleter, Gijs ; McFarland, Sarah ; Bach, Alex ; Bernabucci, Umberto ; Bikker, Paul ; Busani, Luca ; Kok, Esther ; Kostov, Kaloyan ; Nadal, Anna ; Pla, Maria ; Ronchi, Bruno ; Terre, Marta ; Einspanier, Ralf - \ 2018
Food and Chemical Toxicology 117 (2018). - ISSN 0278-6915 - p. 66 - 78.
Feed production chain - Genetically modified crops - Livestock - Post-market monitoring - Regulation - Traceability
This review, which has been prepared within the frame of the European Union (EU)-funded project MARLON, surveys the organisation and characteristics of specific livestock and feed production chains (conventional, organic, GM-free) within the EU, with an emphasis on controls, regulations, traceability, and common production practices. Furthermore, an overview of the origin of animal feed used in the EU as well as an examination of the use of genetically modified organisms (GMOs) in feed is provided. From the data, it shows that livestock is traceable at the herd or individual level, depending on the species. Husbandry practices can vary widely according to geography and animal species, whilst controls and checks are in place for notifiable diseases and general health symptoms (such as mortality, disease, productive performance). For feeds, it would be possible only to make coarse estimates, at best, for the amount of GM feed ingredients that an animal is exposed to. Labeling requirements are apparently correctly followed. Provided that confounding factors are taken into account, practices such as organic agriculture that explicitly involve the use of non-GM feeds could be used for comparison to those involving the use of GM feed.
Exposure of livestock to GM feeds : Detectability and measurement
Nadal, Anna ; Giacomo, Marzia De; Einspanier, Ralf ; Kleter, Gijs ; Kok, Esther ; McFarland, Sarah ; Onori, Roberta ; Paris, Alain ; Toldrà, Mònica ; Dijk, Jeroen van; Wal, Jean Michel ; Pla, Maria - \ 2018
Food and Chemical Toxicology 117 (2018). - ISSN 0278-6915 - p. 13 - 35.
Animal tissue - DNA and protein transfer - Exposure assessment - Genetically modified organism (GMO) - Livestock - Traceability

This review explores the possibilities to determine livestock consumption of genetically modified (GM) feeds/ingredients including detection of genetically modified organism (GMO)-related DNA or proteins in animal samples, and the documentary system that is in place for GM feeds under EU legislation. The presence and level of GMO-related DNA and proteins can generally be readily measured in feeds, using established analytical methods such as polymerase chain reaction and immuno-assays, respectively. Various technical challenges remain, such as the simultaneous detection of multiple GMOs and the identification of unauthorized GMOs for which incomplete data on the inserted DNA may exist. Given that transfer of specific GMO-related DNA or protein from consumed feed to the animal had seldom been observed, this cannot serve as an indicator of the individual animal's prior exposure to GM feeds. To explore whether common practices, information exchange and the specific GM feed traceability system in the EU would allow to record GM feed consumption, the dairy chain in Catalonia, where GM maize is widely grown, was taken as an example. It was thus found that this system would neither enable determination of an animal's consumption of specific GM crops, nor would it allow for quantitation of the exposure.

Erratum to: Western US high June 2015 temperatures and their relation to global warming and soil moisture
Philip, Sjoukje Y. ; Kew, Sarah F. ; Hauser, Mathias ; Guillod, Benoit P. ; Teuling, Adriaan J. ; Whan, Kirien ; Uhe, Peter ; Oldenborgh, Geert Jan Van - \ 2018
Climate Dynamics 50 (2018)7-8. - ISSN 0930-7575 - p. 2603 - 2604.
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