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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Plant functional trait change across a warming tundra biome
Bjorkman, Anne D. ; Myers-Smith, Isla H. ; Elmendorf, Sarah C. ; Normand, Signe ; Rüger, Nadja ; Beck, Pieter S.A. ; Blach-Overgaard, Anne ; Blok, Daan ; Cornelissen, J.H.C. ; Forbes, Bruce C. ; Georges, Damien ; Goetz, Scott J. ; Guay, Kevin C. ; Henry, Gregory H.R. ; Hillerislambers, Janneke ; Hollister, Robert D. ; Karger, Dirk N. ; Kattge, Jens ; Manning, Peter ; Prevéy, Janet S. ; Rixen, Christian ; Schaepman-Strub, Gabriela ; Thomas, Haydn J.D. ; Vellend, Mark ; Wilmking, Martin ; Wipf, Sonja ; Carbognani, Michele ; Hermanutz, Luise ; Lévesque, Esther ; Molau, Ulf ; Petraglia, Alessandro ; Soudzilovskaia, Nadejda A. ; Spasojevic, Marko J. ; Tomaselli, Marcello ; Vowles, Tage ; Alatalo, Juha M. ; Alexander, Heather D. ; Anadon-Rosell, Alba ; Angers-Blondin, Sandra ; Beest, Mariska te; Berner, Logan ; Björk, Robert G. ; Buchwal, Agata ; Buras, Allan ; Christie, Katherine ; Heijmans, Monique M.P.D. ; Ozinga, Wim A. - \ 2018
Nature 526 (2018). - ISSN 0028-0836 - p. 57 - 62.
The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature–trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming.
Extreme precipitation in the Netherlands : An event attribution case study
Eden, Jonathan M. ; Kew, Sarah F. ; Bellprat, Omar ; Lenderink, Geert ; Manola, Iris ; Omrani, Hiba ; Oldenborgh, Geert Jan van - \ 2018
Weather and Climate Extremes 21 (2018). - ISSN 2212-0947 - p. 90 - 101.

Attributing the change in likelihood of extreme weather events, particularly those occurring at small spatiotemporal scales, to anthropogenic forcing is a key challenge in climate science. While a warmer world is associated with an increase in atmospheric moisture on a global scale, the impact on the magnitude of extreme precipitation episodes has substantial regional variability. Analysis of individual cases is important in understanding the extent of these changes on spatial scales relevant to stakeholders. Here, we present a probabilistic attribution analysis of the extreme precipitation that fell in large parts of the Netherlands on 28 July 2014. Using a step-by-step approach, we aim to identify changes in intensity and likelihood of such an event as a result of anthropogenic global warming while highlighting the challenges in performing robust event attribution on high-impact precipitation events that occur at small scales. A method based on extreme value theory is applied to observational data in addition to global and regional climate model ensembles that pass a robust model evaluation process. Results based on observations suggest a strong and significant increase in the intensity and frequency of a 2014-type event as a result of anthropogenic climate change but trends in the model ensembles used are considerably smaller. Our results are communicated alongside considerable uncertainty, highlighting the difficulty in attributing events of this nature. Application of our approach to convection-resolving models may produce a more robust attribution.

Trajectories of the Earth System in the Anthropocene
Steffen, Will ; Rockström, Johan ; Richardson, Katherine ; Lenton, Timothy M. ; Folke, Carl ; Liverman, Diana ; Summerhayes, Colin P. ; Barnosky, Anthony D. ; Cornell, Sarah E. ; Crucifix, Michel ; Donges, Jonathan F. ; Fetzer, Ingo ; Lade, Steven J. ; Scheffer, Marten ; Winkelmann, Ricarda ; Schellnhuber, Hans Joachim - \ 2018
Proceedings of the National Academy of Sciences of the United States of America 115 (2018)33. - ISSN 0027-8424 - p. 8252 - 8259.
Anthropocene - Biosphere feedbacks - Climate change - Earth system trajectories - Tipping elements

We explore the risk that self-reinforcing feedbacks could push the Earth System toward a planetary threshold that, if crossed, could prevent stabilization of the climate at intermediate temperature rises and cause continued warming on a “Hothouse Earth” pathway even as human emissions are reduced. Crossing the threshold would lead to a much higher global average temperature than any interglacial in the past 1.2 million years and to sea levels significantly higher than at any time in the Holocene. We examine the evidence that such a threshold might exist and where it might be. If the threshold is crossed, the resulting trajectory would likely cause serious disruptions to ecosystems, society, and economies. Collective human action is required to steer the Earth System away from a potential threshold and stabilize it in a habitable interglacial-like state. Such action entails stewardship of the entire Earth System—biosphere, climate, and societies—and could include decarbonization of the global economy, enhancement of biosphere carbon sinks, behavioral changes, technological innovations, new governance arrangements, and transformed social values.

Comparison of a laser methane detector with the GreenFeed and two breath analysers for on-farm measurements of methane emissions from dairy cows
Sorg, Diana ; Difford, Gareth F. ; Mühlbach, Sarah ; Kuhla, Björn ; Swalve, Hermann H. ; Lassen, Jan ; Strabel, Tomasz ; Pszczola, Marcin - \ 2018
Computers and Electronics in Agriculture 153 (2018). - ISSN 0168-1699 - p. 285 - 294.
GreenFeed - Laser methane detector - Methane emission - Sniffer

To measure methane (CH4) emissions from cattle on-farm, a number of methods have been developed. Combining measurements made with different methods in one data set could lead to an increased power of further analyses. Before combining the measurements, their agreement must be evaluated. We analysed data obtained with a handheld laser methane detector (LMD) and the GreenFeed system (GF), as well as data obtained with LMD and Fourier Transformed Infrared (FTIR) and Non-dispersive Infrared (NDIR) breath analysers (sniffers) installed in the feed bin of automatic milking systems. These devices record short-term breath CH4 concentrations from cows and make it possible to estimate daily CH4 production in g/d which is used for national CH4 emission inventories and genetic studies. The CH4 is released by cows during eructation and breathing events, resulting in peaks of CH4 concentrations during a measurement which represent the respiratory cycle. For LMD, the average CH4 concentration of all peaks during the measurement (P_MEAN in ppm × meter) was compared with the average daily CH4 production (g/d) measured by GF on 11 cows. The comparison showed a low concordance correlation coefficient (CCC; 0.02) and coefficient of individual agreement (CIA; 0.06) between the methods. The repeated measures correlation (rp) of LMD and GF, which can be seen as a proxy for the genetic correlation, was, however, relatively strong (0.66). Next, based on GF, a prediction equation for estimating CH4 in g/d (LMD_cal) using LMD measurements was developed. LMD_cal showed an improved agreement with GF (CCC = 0.22, CIA = 0.99, rp = 0.74). This prediction equation was used to compare repeated LMD measurements (LMD_val in g/d) with CH4 (g/d) measured with FTIR (n = 34 cows; Data Set A) or NDIR (n = 39 cows; Data Set B) sniffer. A low CCC (A: 0.28; B: 0.17), high CIA (A: 0.91; B: 0.87) and strong rp (A: 0.57; B: 0.60) indicated that there was some agreement and a minimal re-ranking of the cows between sniffer and LMD. Possible sources of disagreement were cow activity (LMD: standing idle; sniffer: eating and being milked) and the larger influence of wind speed on LMD measurement. The LMD measurement was less repeatable (0.14–0.27) than the other techniques studied (0.47–0.77). Nevertheless, GF, LMD and the sniffers ranked the cows similarly. The LMD, due to its portability and flexibility, could be used to study CH4 emissions on herd or group level, as a validation tool, or to strengthen estimates of genetic relationships between small-scale research populations.

Crop traits drive soil carbon sequestration under organic farming
García-Palacios, Pablo ; Gattinger, Andreas ; Bracht-Jørgensen, Helene ; Brussaard, Lijbert ; Carvalho, Filipe ; Castro, Helena ; Clément, Jean Christophe ; Deyn, Gerlinde De; Hertefeldt, Tina D'; Foulquier, Arnaud ; Hedlund, Katarina ; Lavorel, Sandra ; Legay, Nicolas ; Lori, Martina ; Mäder, Paul ; Martínez-García, Laura B. ; Martins da Silva, Pedro ; Muller, Adrian ; Nascimento, Eduardo ; Reis, Filipa ; Symanczik, Sarah ; Paulo Sousa, José ; Milla, Rubén - \ 2018
Journal of Applied Ecology 55 (2018)5. - ISSN 0021-8901 - p. 2496 - 2505.
climate change mitigation - crop residue - ecological intensification - leaf nitrogen - meta-analysis - organic farming - resource economics traits - soil carbon stocks

Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role. To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta-analysis with field measurements across a European-wide network of sites. In the meta-analysis, we related crop species averages of leaf N, leaf-dry matter content, fine-root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management-induced changes in SOC stocks and leaf litter traits after long-term ecological intensive (e.g. OF) vs. CF comparisons. Our global meta-analysis showed that the positive OF-effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF-effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks. Our results highlight that crop species displaying traits indicative of resource-acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites. Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.

Survey of tools for measuring in vivo photosynthesis
Walker, Berkley J. ; Busch, Florian A. ; Driever, Steven M. ; Kromdijk, Johannes ; Lawson, Tracy - \ 2018
In: Photosynthesis / Covshoff, Sarah, New York : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493977857 - p. 3 - 24.
Chlorophyll fluorescence - CO exchange - O exchange - Online mass spectrometry - Photosynthesis
Measurements of in vivo photosynthesis are powerful tools that probe the largest fluxes of carbon and energy in an illuminated leaf, but often the specific techniques used are so varied and specialized that it is difficult for researchers outside the field to select and perform the most useful assays for their research questions. The goal of this chapter is to provide a broad overview of the current tools available for the study of in vivo photosynthesis so as to provide a foundation for selecting appropriate techniques, many of which are presented in detail in subsequent chapters. This chapter also organizes current methods into a comparative framework and provides examples of how they have been applied to research questions of broad agronomical, ecological, or biological importance. The chapter closes with an argument that the future of in vivo measurements of photosynthesis lies in the ability to use multiple methods simultaneously and discusses the benefits of this approach to currently open physiological questions. This chapter, combined with the relevant methods chapters, could serve as a laboratory course in methods in photosynthesis research or as part of a more comprehensive laboratory course in general plant physiology methods.
Management Options for Dealing with Changing Forest-Water Relations
Vira, Bhaskar ; Ellison, David ; McNulty, Steven ; Archer, E. ; Bishop, Kevin ; Claassen, Marius ; Creed, Irena F. ; Gush, Mark ; Gyawali, Dipak ; Martin-Ortega, Julia ; Mukherji, A. ; Murdiyarso, Daniel ; Ovando Pol, Paola ; Sullivan, Caroline A. ; Noordwijk, M. van; Wei, Xiaohua ; Xu, Jianchu ; Reed, Maureen G. ; Wilson, Sarah J. - \ 2018
In: Forest and Water on a Changing Planet: Vulnerability, Adaptation and Governance Opportunities / Creed, Irena F., van Noordwijk, Meine, International Union of Forest Research Organizations (IUFRO) (IUFRO World Series ) - ISBN 9783902762955 - p. 122 - 141.
Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation
Remmers, Ilse M. ; Adamo, Sarah D'; Martens, Dirk E. ; Vos, Ric C.H. de; Mumm, Roland ; America, Antoine H.P. ; Cordewener, Jan H.G. ; Bakker, Linda V. ; Peters, Sander A. ; Wijffels, René H. ; Lamers, Packo P. - \ 2018
Algal Research 35 (2018). - ISSN 2211-9264 - p. 33 - 49.
Diatoms - Diurnal metabolism - Lipids - Mitochondrion - Omics - Triacylglycerol

Nitrogen deprivation increases the triacylglycerol (TAG) content in microalgae but also severely decreases the growth rate. Most approaches that attempted to increase TAG productivity by overexpression or knockdown of specific genes related to the regulation of the lipid synthesis have reported only little success. More insight into the molecular mechanisms related to lipid accumulation and impaired growth rate is needed to find targets for improving TAG productivity. By using the emerging “omics” approach, we comprehensively profiled the physiology, transcriptome, proteome and metabolome of the diatom Phaeodactylum tricornutum during steady state growth at both nitrogen limited and replete levels during light:dark cycles. Under nitrogen limited conditions, 22% (2699) of the total identified transcripts, 17% (543) of the proteins and 44% (345) of the metabolites were significantly differentially regulated compared to nitrogen replete growth conditions. Although nitrogen limitation was responsible for the majority of significant differential transcript, protein and metabolite accumulation, we also observed differential expression over a diurnal cycle. Nitrogen limitation mainly induced an upregulation of nitrogen fixation, central carbon metabolism and TCA cycle, while photosynthetic and ribosomal protein synthesis are mainly downregulated. Regulation of the lipid metabolism and the expression of predicted proteins involved in lipid processes suggest that lipid rearrangements may substantially contribute to TAG distribution. However, TAG synthesis is also limited by the reduced carbon flux through central metabolism. Future strain improvements should therefore focus on understanding and improving the carbon flux through central carbon metabolism, selectivity and activity of DGAT isoforms and lipase enzymes.

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 - p. 291 - 301.
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
Wageningen 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.

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