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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    Modelling food security : Bridging the gap between the micro and the macro scale
    Müller, Birgit ; Hoffmann, Falk ; Heckelei, Thomas ; Müller, Christoph ; Hertel, Thomas W. ; Polhill, J.G. ; Wijk, Mark van; Achterbosch, Thom ; Alexander, Peter ; Brown, Calum ; Kreuer, David ; Ewert, Frank ; Ge, Jiaqi ; Millington, James D.A. ; Seppelt, Ralf ; Verburg, Peter H. ; Webber, Heidi - \ 2020
    Global environmental change : human and policy dimensions 63 (2020). - ISSN 0959-3780
    Agent-based models - Crop models - Economic equilibrium models - Food security - Land use - Model integration - Multi-scale interactions - Social-ecological feedbacks

    Achieving food and nutrition security for all in a changing and globalized world remains a critical challenge of utmost importance. The development of solutions benefits from insights derived from modelling and simulating the complex interactions of the agri-food system, which range from global to household scales and transcend disciplinary boundaries. A wide range of models based on various methodologies (from food trade equilibrium to agent-based) seek to integrate direct and indirect drivers of change in land use, environment and socio-economic conditions at different scales. However, modelling such interaction poses fundamental challenges, especially for representing non-linear dynamics and adaptive behaviours. We identify key pieces of the fragmented landscape of food security modelling, and organize achievements and gaps into different contextual domains of food security (production, trade, and consumption) at different spatial scales. Building on in-depth reflection on three core issues of food security – volatility, technology, and transformation – we identify methodological challenges and promising strategies for advancement. We emphasize particular requirements related to the multifaceted and multiscale nature of food security. They include the explicit representation of transient dynamics to allow for path dependency and irreversible consequences, and of household heterogeneity to incorporate inequality issues. To illustrate ways forward we provide good practice examples using meta-modelling techniques, non-equilibrium approaches and behavioural-based modelling endeavours. We argue that further integration of different model types is required to better account for both multi-level agency and cross-scale feedbacks within the food system.

    Frozen evolution of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
    Pascall, David J. ; Nomikou, Kyriaki ; Bréard, Emmenuel ; Zientara, Stephan ; Silva Filipe, Ana da; Hoffmann, Bernd ; Jacquot, Maude ; Singer, Joshua B. ; Clercq, Kris De; Botner, Anette ; Sailleau, Corinne ; Viarouge, Cyril ; Batten, Carrie ; Puggioni, Giantonella ; Ligios, Ciriaco ; Savini, Giovanni ; Rijn, P.A. van; Mertens, Peter P.C. ; Biek, Roman ; Palmarini, Massimo - \ 2020
    PloS Biology (2020). - ISSN 1545-7885
    Broadening the miRNA catalogue in livestock species: A contribution to the functional annotation of animal genomes.
    Amaral, A.J. ; Anthon, C. ; Corsi, G. ; Vasconcelos, A. ; Marthey, Sylvain ; Hoffmann, A. ; Lagnel, Jacques ; Haack, Fiete ; Pokharel, Kisun ; Palasca, O. ; Seemann, S.E. ; Gama, Luis ; Groenen, M. ; Kantanen, Juha ; Crooijmans, R.P.M.A. ; Rijnkels, M. ; Kalbfleisch, T. ; Giuffra, Elisabetta ; Stadler, P.F. ; Madsen, O. ; Gorodkin, J. - \ 2019
    In: ISAG 2019 Abstracts Book. - - p. 51 - 52.
    MicroRNAs play a crucial role in the regulation of gene expression. Their action is crucial in many biological processes and functions, such as cell development
    and differentiation, and in response to disease. Moreover, it has been shown that polymorphisms in miRNAs can be linked to diseases and complex traits. An improved annotation of miRNAs in domestic animals is therefore required to acquire a comprehensive understanding of their impact on livestock traits. There are a large number of published studies with public data sets across most of livestock species and covering a wide range of tissues. However there have been few resources to capitalize on these data to better understand these features, distribution and biogenesis in these genomes. Therefore, a working group was established for the development of analysis pipelines and methods of data analysis of small-RNA-seq data in the framework of COST-Action FAANG-Europe. A total of 846 quality ap- proved small-RNA-seq data sets available from public repositories for 6 livestock species (Gallus gallus, Sus scrofa, Equus caballus, Ovis aries, Capra hircus and Bos taurus) were used to quantify miRNA expression in different tissues as well as to identify putative novel miRNA candidates. Our analyses has identified across the 6 species a total of 1,404 novel pre-miRNAs, with a larger impact for Bos taurus and Sus scrofa, in which these represent an increase of 50% for these species in comparison with miRBase v22. We will use these to perform large-scale analysis of miRNA function and biogenesis. These analyses will include global expression comparison, co-expression of miRNA clusters. Additionally we will report for the first time in these tissues a global analysis of miRNA epi-transcriptomic modifications and access their prevalence across species and tissues. We believe these findings will further contribute to the understanding of the functional genome of the studied species. AJA is supported by a post-doctoral fellowship within IMAGE H2020 project (REF 677353–2). This abstract is based upon the work from COST Action FAANG-Europe (CA15112) supported by COST (European Cooperation in Science and technology) and co-funded by FCT grant UID/CVT/00276/2013.
    Can Advertising Investments Counter the Negative Impact of Shareholder Complaints on Firm Value?
    Wies, Simone ; Hoffmann, Arvid Oskar Ivar ; Aspara, Jaakko ; Pennings, Joost M.E. - \ 2019
    Journal of Marketing 83 (2019)4. - ISSN 0022-2429 - p. 58 - 80.
    Shareholder complaints put pressure on publicly listed firms, yet firms rarely directly address the actual issues raised in these complaints. The authors examine whether firms respond in an alternative way by altering advertising investments in an effort to ward off the financial damage associated with shareholder complaints. By analyzing a unique data set of shareholder complaints submitted to S&P 1500 firms between 2001 and 2016, supplemented with qualitative interviews of executives of publicly listed firms, the authors document that firms increase advertising investments following shareholder complaints and that such an advertising investment response mitigates a postcomplaint decline in firm value. Furthermore, results suggest that firms are more likely to increase advertising investments when shareholder complaints are submitted by institutional investors, pertain to nonfinancial concerns, and relate to topics that receive high media attention. The findings provide new insights on how firms address stock market adversities with advertising investments and inform managers about the effectiveness of such a response.
    What’s Cooking in Berlin’s Food Policy Kitchen
    Hoffmann, Dinah ; Morrow, Oona ; Pohl, Christine - \ 2019
    Urban Agriculture Magazine (2019)36. - ISSN 1571-6244 - p. 37 - 39.
    After years of silence on municipal food policy in Berlin, actors from civil society, academia, industry and the local senate have come together to discuss the current state and future of Berlin’s food system, and are developing the city’s first urban food strategy. The Ernährungsrat Berlin is the citizen-led urban food policy council working towards food democracy and re-localisation in the Berlin-Brandenburg region.
    An emulator approach to stratocumulus susceptibility
    Glassmeier, Franziska ; Hoffmann, Fabian ; Johnson, Jill S. ; Yamaguchi, Takanobu ; Carslaw, Ken S. ; Feingold, Graham - \ 2019
    Atmospheric Chemistry and Physics 19 (2019)15. - ISSN 1680-7316 - p. 10191 - 10203.

    The climatic relevance of aerosol-cloud interactions depends on the sensitivity of the radiative effect of clouds to cloud droplet number N, and liquid water path LWP. We derive the dependence of cloud fraction CF, cloud albedo AC, and the relative cloud radiative effect rCRE D CF • AC on N and LWP from 159 large-eddy simulations of nocturnal stratocumulus. These simulations vary in their initial conditions for temperature, moisture, boundary-layer height, and aerosol concentration but share boundary conditions for surface fluxes and subsidence. Our approach is based on Gaussian-process emulation, a statistical technique related to machine learning. We succeed in building emulators that accurately predict simulated values of CF, AC, and rCRE for given values of N and LWP. Emulator-derived susceptibilities @ lnrCRE=@ lnN and @ lnrCRE=@ lnLWP cover the nondrizzling, fully overcast regime as well as the drizzling regime with broken cloud cover. Theoretical results, which are limited to the nondrizzling regime, are reproduced. The susceptibility @ lnrCRE=@ lnN captures the strong sensitivity of the cloud radiative effect to cloud fraction, while the susceptibility @ lnrCRE=@ lnLWP describes the influence of cloud amount on cloud albedo irrespective of cloud fraction. Our emulation-based approach provides a powerful tool for summarizing complex data in a simple framework that captures the sensitivities of cloud-field properties over a wide range of states.

    Predicting the spatial dynamics of Wolbachia infections in Aedes aegypti arbovirus vector populations in heterogeneous landscapes
    Hancock, Penelope A. ; Ritchie, Scott A. ; Koenraadt, Constantianus J.M. ; Scott, Thomas W. ; Hoffmann, Ary A. ; Godfray, Charles - \ 2019
    Journal of Applied Ecology 56 (2019)7. - ISSN 0021-8901 - p. 1674 - 1686.
    arbovirus - dengue - gene drive - spatial spread - wAlbB - wMel - wMelPop - Zika

    A promising strategy for reducing the transmission of dengue and other arboviral human diseases by Aedes aegypti mosquito vector populations involves field introductions of the endosymbiotic bacteria Wolbachia. Wolbachia infections inhibit viral transmission by the mosquito, and can spread between mosquito hosts to reach high frequencies in the vector population. Wolbachia spreads by maternal transmission, and spread dynamics can be variable and highly dependent on natural mosquito population dynamics, population structure and fitness components. We develop a mathematical model of an A. aegypti metapopulation that incorporates empirically validated relationships describing density-dependent mosquito fitness components. We assume that density dependent relationships differ across subpopulations, and construct heterogeneous landscapes for which model-predicted patterns of variation in mosquito abundance and demography approximate those observed in field populations. We then simulate Wolbachia release strategies similar to that used in field trials. We show that our model can produce rates of spatial spread of Wolbachia similar to those observed following field releases. We then investigate how different types of spatio-temporal variation in mosquito habitat, as well as different fitness costs incurred by Wolbachia on the mosquito host, influence predicted spread rates. We find that fitness costs reduce spread rates more strongly when the habitat landscape varies temporally due to stochastic and seasonal processes. Synthesis and applications: Our empirically based modelling approach represents effects of environmental heterogeneity on the spatial spread of Wolbachia. The models can assist in interpreting observed spread patterns following field releases and in designing suitable release strategies for targeting spatially heterogeneous vector populations.

    Highly Porous Nanocrystalline UiO-66 Thin Films via Coordination Modulation Controlled Step-by-Step Liquid-Phase Growth
    Semrau, A.L. ; Wannapaiboon, Suttipong ; Pujari, Sidharam P. ; Vervoorts, Pia ; Albada, Bauke ; Zuilhof, Han ; Fischer, Roland A. - \ 2019
    Crystal Growth and Design 19 (2019)3. - ISSN 1528-7483 - p. 1738 - 1747.

    Metal-organic frameworks (MOFs) possess exciting properties, which can be tailored by rational material design approaches. Integration of MOFs in functional nano- and mesoscale systems require selective crystallite positioning and thin-film growth techniques. Stepwise layer-by-layer liquid-phase epitaxy (LPE) emerged as one of the methods of choice to fabricate MOF@substrate systems. The layer-by-layer approach of LPE allows a precise control over the film thickness and crystallite orientation. However, these advantages were mostly observed in cases of tetra-connected dinuclear paddle-wheel MOFs and Hoffmann-type MOFs. Higher connected MOFs (consisting of nodes with 8-12 binding sites), such as the Zr-oxo cluster based families, are notoriously hard to deposit in an acceptable quality by the stepwise liquid-phase process. Herein, we report the use of coordination modulation (CM) to assist and enhance the LPE growth of UiO-66, Zr 6 O 4 (OH) 4 (bdc) 6 (bdc 2- = 1,4-benzene-dicarboxylate) films. Highly porous and crystalline thin films were obtained with good control of the crystallite domain size and film thickness in the nanoscale regime. The crystallinity (by grazing incidence X-ray diffraction), morphology (by scanning electron microscopy, atomic form microscopy), elemental composition (by X-ray photoelectron spectroscopy), binding properties (by infrared spectroscopy), and adsorption capacity (by quartz crystal microbalance adsorption experiments) for volatile organic compounds (e.g. CH 3 OH) of the fabricated thin films were investigated. These results substantiate a proof-of-concept of CM-LPE of MOFs and could be the gateway to facilitate in general the deposition of chemically very robust and higher-connected MOF thin films with automatic process-controlled LPE techniques under mild synthetic conditions.

    Implications of crop model ensemble size and composition for estimates of adaptation effects and agreement of recommendations
    Rodríguez, A. ; Ruiz-Ramos, M. ; Palosuo, T. ; Carter, T.R. ; Fronzek, S. ; Lorite, I.J. ; Ferrise, R. ; Pirttioja, N. ; Bindi, M. ; Baranowski, P. ; Buis, S. ; Cammarano, D. ; Chen, Y. ; Dumont, B. ; Ewert, F. ; Gaiser, T. ; Hlavinka, P. ; Hoffmann, H. ; Höhn, J.G. ; Jurecka, F. ; Kersebaum, K.C. ; Krzyszczak, J. ; Lana, M. ; Mechiche-Alami, A. ; Minet, J. ; Montesino, M. ; Nendel, C. ; Porter, J.R. ; Ruget, F. ; Semenov, M.A. ; Steinmetz, Z. ; Stratonovitch, P. ; Supit, I. ; Tao, F. ; Trnka, M. ; Wit, A. de; Rötter, R.P. - \ 2019
    Agricultural and Forest Meteorology 264 (2019). - ISSN 0168-1923 - p. 351 - 362.
    Climate change - Decision support - Outcome confidence - Response surface - Uncertainty - Wheat adaptation

    Climate change is expected to severely affect cropping systems and food production in many parts of the world unless local adaptation can ameliorate these impacts. Ensembles of crop simulation models can be useful tools for assessing if proposed adaptation options are capable of achieving target yields, whilst also quantifying the share of uncertainty in the simulated crop impact resulting from the crop models themselves. Although some studies have analysed the influence of ensemble size on model outcomes, the effect of ensemble composition has not yet been properly appraised. Moreover, results and derived recommendations typically rely on averaged ensemble simulation results without accounting sufficiently for the spread of model outcomes. Therefore, we developed an Ensemble Outcome Agreement (EOA) index, which analyses the effect of changes in composition and size of a multi-model ensemble (MME) to evaluate the level of agreement between MME outcomes with respect to a given hypothesis (e.g. that adaptation measures result in positive crop responses). We analysed the recommendations of a previous study performed with an ensemble of 17 crop models and testing 54 adaptation options for rainfed winter wheat (Triticum aestivum L.) at Lleida (NE Spain) under perturbed conditions of temperature, precipitation and atmospheric CO2 concentration. Our results confirmed that most adaptations recommended in the previous study have a positive effect. However, we also showed that some options did not remain recommendable in specific conditions if different ensembles were considered. Using EOA, we were able to identify the adaptation options for which there is high confidence in their effectiveness at enhancing yields, even under severe climate perturbations. These include substituting spring wheat for winter wheat combined with earlier sowing dates and standard or longer duration cultivars, or introducing supplementary irrigation, the latter increasing EOA values in all cases. There is low confidence in recovering yields to baseline levels, although this target could be attained for some adaptation options under moderate climate perturbations. Recommendations derived from such robust results may provide crucial information for stakeholders seeking to implement adaptation measures.

    Meta-analysis of genome-wide association studies of aggressive and chronic periodontitis identifies two novel risk loci
    Munz, Matthias ; Richter, Gesa M. ; Loos, Bruno G. ; Jepsen, Søren ; Divaris, Kimon ; Offenbacher, Steven ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Bruckmann, Corinna ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Ahmad, Ilyas ; Staufenbiel, Ingmar ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette C.P.G.M. De; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Laudes, Matthias ; Lieb, Wolfgang ; Franke, Andre ; Erdmann, Jeanette ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2019
    European Journal of Human Genetics 27 (2019)1. - ISSN 1018-4813 - p. 102 - 113.
    Periodontitis is one of the most common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an estimated heritability of 50%. It is classified into the widespread moderate form chronic periodontitis (CP) and the rare early-onset and severe phenotype aggressive periodontitis (AgP). These different disease manifestations are thought to share risk alleles and predisposing environmental factors. To obtain novel insights into the shared genetic etiology and the underlying molecular mechanisms of both forms, we performed a two step-wise meta-analysis approach using genome-wide association studies of both phenotypes. Genotypes from imputed genome-wide association studies (GWAS) of AgP and CP comprising 5,095 cases and 9,908 controls of North-West European genetic background were included. Two loci were associated with periodontitis at a genome-wide significance level. They located within the pseudogene MTND1P5 on chromosome 8 (rs16870060-G, P = 3.69 × 10−9, OR = 1.36, 95% CI = [1.23–1.51]) and intronic of the long intergenic non-coding RNA LOC107984137 on chromosome 16, downstream of the gene SHISA9 (rs729876-T, P = 9.77 × 10−9, OR = 1.24, 95% CI = [1.15–1.34]). This study identified novel risk loci of periodontitis, adding to the genetic basis of AgP and CP.
    The American Inventors Protection Act: A Natural Experiment on Innovation Disclosure and the Cost of Debt
    Hoffmann, Arvid O.I. ; Kleimeier, Stefanie ; Mimiroglu, Nagihan ; Pennings, Joost M.E. - \ 2019
    International Review of Finance 19 (2019)3. - ISSN 1369-412X - p. 641 - 651.
    We examine the impact of innovation disclosure through patenting on firms' cost of debt, focusing on the American Inventors Protection Act (AIPA) as an exogenous shock in innovation disclosure regulation. Post-AIPA, firms have an incentive to apply for patents only if commercial success is likely. Accordingly, we expect post-AIPA patents to be a better proxy for successful innovation activity, and thus to have a stronger effect on reducing the cost of debt than pre-AIPA patents. Indeed, we find that pre-AIPA patents reduce the cost of debt only for the most innovative firms, while post-AIPA, this effect holds for all firms.
    Broadening the miRNA Catalogue in Livestock Species
    Amaral, A.J. ; Marthey, Sylvain ; Hoffmann, A. ; Lagnel, Jacques ; Haack, Fiete ; Pokharel, Kisun ; Palasca, O. ; Stadler, P.F. ; Anthon, C. ; Seemann, S.E. ; Arya, Anoop ; Gama, Luis ; Groenen, Martien ; Kantanen, Juha ; Crooijmans, Richard ; Giuffra, Elisabetta ; Madsen, Ole ; Gorodkin, J. - \ 2018
    Powerpoint presentation
    Prevalence of tick-borne viruses in Ixodes ricinus assessed by high-throughput real-time PCR
    Gondard, Mathilde ; Michelet, Lorraine ; Nisavanh, Athinna ; Devillers, Elodie ; Delannoy, Sabine ; Fach, Patrick ; Aspan, Anna ; Ullman, Karin ; Chirico, Jan ; Hoffmann, Bernd ; Wal, Fimme Jan van der; Koeijer, Aline de; Solt-Smits, Conny van; Jahfari, Seta ; Sprong, Hein ; Mansfield, Karen L. ; Fooks, Anthony R. ; Klitgaard, Kirstine ; Bødker, Rene ; Moutailler, Sara - \ 2018
    Pathogens and Disease 76 (2018)8. - ISSN 2049-632X
    Europe - microfluidic analysis - molecular epidemiology - surveillance - tick borne viruses

    Ticks are one of the principal arthropod vectors of human and animal infectious diseases. Whereas the prevalence of tick-borne encephalitis virus in ticks in Europe is well studied, there is less information available on the prevalence of the other tick-borne viruses (TBVs) existing worldwide. The aim of this study was to improve the epidemiological survey tools of TBVs by the development of an efficient high-throughput test to screen a wide range of viruses in ticks. In this study, we developed a new high-throughput virus-detection assay based on parallel real-time PCRs on a microfluidic system, and used it to perform a large scale epidemiological survey screening for the presence of 21 TBVs in 18 135 nymphs of Ixodes ricinus collected from five European countries. This extensive investigation has (i) evaluated the prevalence of four viruses present in the collected ticks, (ii) allowed the identification of viruses in regions where they were previously undetected. In conclusion, we have demonstrated the capabilities of this new screening method that allows the detection of numerous TBVs in a large number of ticks. This tool represents a powerful and rapid system for TBVs surveillance in Europe and could be easily customized to assess viral emergence.

    Integration of Murine and Human Studies for Mapping Periodontitis Susceptibility
    Nashef, A. ; Qabaja, R. ; Salaymeh, Y. ; Botzman, M. ; Munz, M. ; Dommisch, H. ; Krone, B. ; Hoffmann, P. ; Wellmann, J. ; Laudes, M. ; Berger, K. ; Kocher, T. ; Loos, B. ; Velde, N. van der; Uitterlinden, A.G. ; Groot, L.C.P.G.M. de; Franke, A. ; Offenbacher, S. ; Lieb, W. ; Divaris, K. ; Mott, R. ; Gat-Viks, I. ; Wiess, E. ; Schaefer, A. ; Iraqi, F.A. ; Haddad, Y.H. - \ 2018
    Journal of Dental Research 97 (2018)5. - ISSN 0022-0345 - p. 537 - 546.
    alveolar bone loss - animal model - Collaborative Cross - genetic - GWAS - QTL mapping

    Periodontitis is one of the most common inflammatory human diseases with a strong genetic component. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWASs) of chronic periodontitis (CP) have largely been unsuccessful in identifying common susceptibility factors. A combination of quantitative trait loci (QTL) mapping in mice with association studies in humans has the potential to discover novel risk loci. To this end, we assessed alveolar bone loss in response to experimental periodontal infection in 25 lines (286 mice) from the Collaborative Cross (CC) mouse population using micro–computed tomography (µCT) analysis. The orthologous human chromosomal regions of the significant QTL were analyzed for association using imputed genotype data (OmniExpress BeadChip arrays) derived from case-control samples of aggressive periodontitis (AgP; 896 cases, 7,104 controls) and chronic periodontitis (CP; 2,746 cases, 1,864 controls) of northwest European and European American descent, respectively. In the mouse genome, QTL mapping revealed 2 significant loci (–log P = 5.3; false discovery rate = 0.06) on chromosomes 1 (Perio3) and 14 (Perio4). The mapping resolution ranged from ~1.5 to 3 Mb. Perio3 overlaps with a previously reported QTL associated with residual bone volume in F2 cross and includes the murine gene Ccdc121. Its human orthologue showed previously a nominal significant association with CP in humans. Use of variation data from the genomes of the CC founder strains further refined the QTL and suggested 7 candidate genes (CAPN8, DUSP23, PCDH17, SNORA17, PCDH9, LECT1, and LECT2). We found no evidence of association of these candidates with the human orthologues. In conclusion, the CC populations enabled mapping of confined QTL that confer susceptibility to alveolar bone loss in mice and larger human phenotype-genotype samples and additional expression data from gingival tissues are likely required to identify true positive signals.

    Genome-wide association meta-analysis of coronary artery disease and periodontitis reveals a novel shared risk locus
    Munz, Matthias ; Richter, Gesa M. ; Loos, Bruno G. ; Jepsen, Søren ; Divaris, Kimon ; Offenbacher, Steven ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Bruckmann, Corinna ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Munoz, Loreto ; Bhandari, Anita ; Tennstedt, Stephanie ; Staufenbiel, Ingmar ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, Lisette C.P.G.M. De; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Laudes, Matthias ; Lieb, Wolfgang ; Franke, Andre ; Dommisch, Henrik ; Erdmann, Jeanette ; Schaefer, Arne S. - \ 2018
    Scientific Reports 8 (2018)1. - ISSN 2045-2322
    Evidence for a shared genetic basis of association between coronary artery disease (CAD) and periodontitis (PD) exists. To explore the joint genetic basis, we performed a GWAS meta-analysis. In the discovery stage, we used a German aggressive periodontitis sample (AgP-Ger; 680 cases vs 3,973 controls) and the CARDIoGRAMplusC4D CAD meta-analysis dataset (60,801 cases vs 123,504 controls). Two SNPs at the known CAD risk loci ADAMTS7 (rs11634042) and VAMP8 (rs1561198) passed the pre-assigned selection criteria (PAgP-Ger < 0.05; PCAD < 5 × 10−8; concordant effect direction) and were replicated in an independent GWAS meta-analysis dataset of PD (4,415 cases vs 5,935 controls). SNP rs1561198 showed significant association (PD[Replication]: P = 0.008 OR = 1.09, 95% CI = [1.02–1.16]; PD [Discovery + Replication]: P = 0.0002, OR = 1.11, 95% CI = [1.05–1.17]). For the associated haplotype block, allele specific cis-effects on VAMP8 expression were reported. Our data adds to the shared genetic basis of CAD and PD and indicate that the observed association of the two disease conditions cannot be solely explained by shared environmental risk factors. We conclude that the molecular pathway shared by CAD and PD involves VAMP8 function, which has a role in membrane vesicular trafficking, and is manipulated by pathogens to corrupt host immune defense.
    Arabidopsis phospholipase C3 is involved in lateral root initiation and ABA responses in seed germination and stomatal closure
    Zhang, Qianqian ; Wijk, Ringo van; Shahbaz, Muhammad ; Roels, Wendy ; Schooten, Bas Van; Vermeer, Joop E.M. ; Zarza, Xavier ; Guardia, Aisha ; Scuffi, Denise ; García-Mata, Carlos ; Laha, Debabrata ; Williams, Phoebe ; Willems, Leo A.J. ; Ligterink, Wilco ; Hoffmann-Benning, Susanne ; Gillaspy, Glenda ; Schaaf, Gabriel ; Haring, Michel A. ; Laxalt, Ana M. ; Munnik, Teun - \ 2018
    Plant and Cell Physiology 59 (2018)3. - ISSN 0032-0781 - p. 469 - 486.
    ABA - Arabidopsis - Drought tolerance - Lateral root formation - Seed germination - Stomatal closure

    Phospholipase C (PLC) is well known for its role in animal signaling, where it generates the second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG), by hydrolyzing the minor phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2), upon receptor stimulation. In plants, PLC's role is still unclear, especially because the primary targets of both second messengers are lacking, i.e. the ligand-gated Ca2+ channel and protein kinase C, and because PIP2 levels are extremely low. Nonetheless, the Arabidopsis genome encodes nine PLCs. We used a reversed-genetic approach to explore PLC's function in Arabidopsis, and report here that PLC3 is required for proper root development, seed germination and stomatal opening. Two independent knock-down mutants, plc3-2 and plc3-3, were found to exhibit reduced lateral root densities by 10-20%. Mutant seeds germinated more slowly but were less sensitive to ABA to prevent germination. Guard cells of plc3 were also compromised in ABA-dependent stomatal closure. Promoter-b-glucuronidase (GUS) analyses confirmed PLC3 expression in guard cells and germinating seeds, and revealed that the majority is expressed in vascular tissue, most probably phloem companion cells, in roots, leaves and flowers. In vivo 32Pi labeling revealed that ABA stimulated the formation of PIP2 in germinating seeds and guard cell-enriched leaf peels, which was significantly reduced in plc3 mutants. Overexpression of PLC3 had no effect on root system architecture or seed germination, but increased the plant's tolerance to drought. Our results provide genetic evidence for PLC's involvement in plant development and ABA signaling, and confirm earlier observations that overexpression increases drought tolerance. Potential molecular mechanisms for the above observations are discussed.

    Impacts of climate change adaptation options on soil functions: A review of European case-studies
    Hamidov, Ahmad ; Helming, Katharina ; Bellocchi, Gianni ; Bojar, Waldemar ; Dalgaard, Tommy ; Ghaley, Bhim Bahadur ; Hoffmann, Christian ; Holman, Ian ; Holzkämper, Annelie ; Krzeminska, Dominika ; Kvaernø, Sigrun H. ; Lehtonen, Heikki ; Niedrist, Georg ; Øygarden, Lillian ; Reidsma, Pytrik ; Roggero, Pier Paolo ; Rusu, Teodor ; Santos, Cristina ; Seddaiu, Giovanna ; Skarbøvik, Eva ; Ventrella, Domenico ; Żarski, Jacek ; Schönhart, Martin - \ 2018
    Land Degradation and Development 29 (2018)8. - ISSN 1085-3278 - p. 2378 - 2389.
    Soils are vital for supporting food security and other ecosystem services. Climate change can affect soil functions both directly and indirectly. Direct effects include temperature, precipitation, and moisture regime changes. Indirect effects include those that are induced by adaptations such as irrigation, crop rotation changes, and tillage practices. Although extensive knowledge is available on the direct effects, an understanding of the indirect effects of agricultural adaptation options is less complete. A review of 20 agricultural adaptation case‐studies across Europe was conducted to assess implications to soil threats and soil functions and the link to the Sustainable Development Goals (SDGs). The major findings are as follows: (a) adaptation options reflect local conditions; (b) reduced soil erosion threats and increased soil organic carbon are expected, although compaction may increase in some areas; (c) most adaptation options are anticipated to improve the soil functions of food and biomass production, soil organic carbon storage, and storing, filtering, transforming, and recycling capacities, whereas possible implications for soil biodiversity are largely unknown; and (d) the linkage between soil functions and the SDGs implies improvements to SDG 2 (achieving food security and promoting sustainable agriculture) and SDG 13 (taking action on climate change), whereas the relationship to SDG 15 (using terrestrial ecosystems sustainably) is largely unknown. The conclusion is drawn that agricultural adaptation options, even when focused on increasing yields, have the potential to outweigh the negative direct effects of climate change on soil degradation in many European regions.
    Perception of livestock ecosystem services in grazing areas
    Leroy, G. ; Hoffmann, I. ; From, T. ; Hiemstra, S.J. ; Gandini, G. - \ 2018
    Animal 12 (2018)12. - ISSN 1751-7311 - p. 2627 - 2638.
    breed - multivariate analysis - survey - sustainability
    This study investigates how the ecosystem services (ES) linked to livestock grazing are perceived across countries. A total of 82 case studies collected from 42 countries via survey (53.7% cases from Europe and 46.3% from outside of Europe) have been analysed through a multivariate approach. In all, 18 non-provisioning ES were considered. Overall, the reported impacts of livestock grazing on the different ES were much more positive than negative. Notably, a large proportion of respondents reported either positive or very positive impacts for some cultural ES, namely cultural, historic and natural heritage (84%), knowledge systems and educational values (77%), landscape values (74%), and for some supporting and regulating ES, namely habitat provision (66%), nutrient cycling (65%), and bush encroachment/fire control (66%). Based on multiple regression analysis, geographic origin, stakeholder type and species category, as well as protection status of the grazing area, had significant effects on the perception of the impacts. Respondents reported those impacts as more positive in Europe, in protected areas and where several species were present in the grazing area. A significantly larger proportion of respondents reported recognition of ES provided by the grazing livestock population in European countries (40.9%) compared with non-European countries (23.7%). Based on the survey responses it appears that in non-European countries absence of formal recognition, especially by policy makers, is a major challenge for the continued provision of ES in grazing systems. In Europe, where such recognition is already often included in legislation, the long-term sustainability of related policies and incentives to provide such services is viewed as a major issue by the respondents.
    Corrigendum to: A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis
    Munz, Matthias ; Willenborg, Christina ; Richter, Gesa M. ; Jockel-Schneider, Yvonne ; Graetz, Christian ; Staufenbiel, Ingmar ; Wellmann, Jürgen ; Berger, Klaus ; Krone, Bastian ; Hoffmann, Per ; Velde, Nathalie Van Der; Uitterlinden, André G. ; Groot, C.P.G.M. De; Sawalha, Amr H. ; Direskeneli, Haner ; Saruhan-Direskeneli, Güher ; Guzeldemir-Akcakanat, Esra ; Keceli, Huseyin Gencay ; Laudes, Matthias ; Noack, Barbara ; Teumer, Alexander ; Holtfreter, Birte ; Kocher, Thomas ; Eickholz, Peter ; Meyle, Jörg ; Doerfer, Christof ; Bruckmann, Corinna ; Lieb, Wolfgang ; Franke, Andre ; Schreiber, Stefan ; Nohutcu, Rahime M. ; Erdmann, Jeanette ; Loos, Bruno G. ; Jepsen, Soeren ; Dommisch, Henrik ; Schaefer, Arne S. - \ 2018
    Human Molecular Genetics 27 (2018)5. - ISSN 0964-6906 - p. 941 - 942.
    Classifying multi-model wheat yield impact response surfaces showing sensitivity to temperature and precipitation change
    Fronzek, Stefan ; Pirttioja, Nina ; Carter, Timothy R. ; Bindi, Marco ; Hoffmann, Holger ; Palosuo, Taru ; Ruiz-Ramos, Margarita ; Tao, Fulu ; Trnka, Miroslav ; Acutis, Marco ; Asseng, Senthold ; Baranowski, Piotr ; Basso, Bruno ; Bodin, Per ; Buis, Samuel ; Cammarano, Davide ; Deligios, Paola ; Destain, Marie France ; Dumont, Benjamin ; Ewert, Frank ; Ferrise, Roberto ; François, Louis ; Gaiser, Thomas ; Hlavinka, Petr ; Jacquemin, Ingrid ; Kersebaum, Kurt Christian ; Kollas, Chris ; Krzyszczak, Jaromir ; Lorite, Ignacio J. ; Minet, Julien ; Minguez, M.I. ; Montesino, Manuel ; Moriondo, Marco ; Müller, Christoph ; Nendel, Claas ; Öztürk, Isik ; Perego, Alessia ; Rodríguez, Alfredo ; Ruane, Alex C. ; Ruget, Françoise ; Sanna, Mattia ; Semenov, Mikhail A. ; Slawinski, Cezary ; Stratonovitch, Pierre ; Supit, Iwan ; Waha, Katharina ; Wang, Enli ; Wu, Lianhai ; Zhao, Zhigan ; Rötter, Reimund P. - \ 2018
    Agricultural Systems 159 (2018). - ISSN 0308-521X - p. 209 - 224.
    Classification - Climate change - Crop model - Ensemble - Sensitivity analysis - Wheat

    Crop growth simulation models can differ greatly in their treatment of key processes and hence in their response to environmental conditions. Here, we used an ensemble of 26 process-based wheat models applied at sites across a European transect to compare their sensitivity to changes in temperature (-2 to +9°C) and precipitation (-50 to +50%). Model results were analysed by plotting them as impact response surfaces (IRSs), classifying the IRS patterns of individual model simulations, describing these classes and analysing factors that may explain the major differences in model responses.The model ensemble was used to simulate yields of winter and spring wheat at four sites in Finland, Germany and Spain. Results were plotted as IRSs that show changes in yields relative to the baseline with respect to temperature and precipitation. IRSs of 30-year means and selected extreme years were classified using two approaches describing their pattern.The expert diagnostic approach (EDA) combines two aspects of IRS patterns: location of the maximum yield (nine classes) and strength of the yield response with respect to climate (four classes), resulting in a total of 36 combined classes defined using criteria pre-specified by experts. The statistical diagnostic approach (SDA) groups IRSs by comparing their pattern and magnitude, without attempting to interpret these features. It applies a hierarchical clustering method, grouping response patterns using a distance metric that combines the spatial correlation and Euclidian distance between IRS pairs. The two approaches were used to investigate whether different patterns of yield response could be related to different properties of the crop models, specifically their genealogy, calibration and process description.Although no single model property across a large model ensemble was found to explain the integrated yield response to temperature and precipitation perturbations, the application of the EDA and SDA approaches revealed their capability to distinguish: (i) stronger yield responses to precipitation for winter wheat than spring wheat; (ii) differing strengths of response to climate changes for years with anomalous weather conditions compared to period-average conditions; (iii) the influence of site conditions on yield patterns; (iv) similarities in IRS patterns among models with related genealogy; (v) similarities in IRS patterns for models with simpler process descriptions of root growth and water uptake compared to those with more complex descriptions; and (vi) a closer correspondence of IRS patterns in models using partitioning schemes to represent yield formation than in those using a harvest index.Such results can inform future crop modelling studies that seek to exploit the diversity of multi-model ensembles, by distinguishing ensemble members that span a wide range of responses as well as those that display implausible behaviour or strong mutual similarities.

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