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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Current knowledge and future research opportunities for modeling annual crop mixtures. A review
Gaudio, Noémie ; Escobar-Gutiérrez, Abraham J. ; Casadebaig, Pierre ; Evers, Jochem B. ; Gérard, Frédéric ; Louarn, Gaëtan ; Colbach, Nathalie ; Munz, Sebastian ; Launay, Marie ; Marrou, Hélène ; Barillot, Romain ; Hinsinger, Philippe ; Bergez, Jacques Eric ; Combes, Didier ; Durand, Jean Louis ; Frak, Ela ; Pagès, Loïc ; Pradal, Christophe ; Saint-Jean, Sébastien ; Werf, Wopke van der; Justes, Eric - \ 2019
Agronomy for Sustainable Development 39 (2019)2. - ISSN 1774-0746
Annual crop mixtures - Crop models - Functional–structural plant models - Genotypes mixtures - Individual-based models - Intercrops - Model users

Growing mixtures of annual arable crop species or genotypes is a promising way to improve crop production without increasing agricultural inputs. To design optimal crop mixtures, choices of species, genotypes, sowing proportion, plant arrangement, and sowing date need to be made but field experiments alone are not sufficient to explore such a large range of factors. Crop modeling allows to study, understand, and ultimately design cropping systems and is an established method for sole crops. Recently, modeling started to be applied to annual crop mixtures as well. Here, we review to what extent crop simulation models and individual-based models are suitable to capture and predict the specificities of annual crop mixtures. We argued that (1) the crop mixture spatio-temporal heterogeneity (influencing the occurrence of ecological processes) determines the choice of the modeling approach (plant or crop centered). (2) Only few crop models (adapted from sole crop models) and individual-based models currently exist to simulate annual crop mixtures. Crop models are mainly used to address issues related to both crop mixtures management and the integration of crop mixtures into larger scales such as the rotation. In contrast, individual-based models are mainly used to identify plant traits involved in crop mixture performance and to quantify the relative contribution of the different ecological processes (niche complementarity, facilitation, competition, plasticity) to crop mixture functioning. This review highlights that modeling of annual crop mixtures is in its infancy and gives to model users some important keys to choose the model based on the questions they want to answer, with awareness of the strengths and weaknesses of each of the modeling approaches.

Agriculture versus wastewater pollution as drivers of macroinvertebrate community structure in streams
Burdon, F.J. ; Munz, N.A. ; Reyes, M. ; Focks, A. ; Joss, A. ; Räsänen, K. ; Altermatt, F. ; Eggen, R.I.L. ; Stamm, C. - \ 2019
Science of the Total Environment 659 (2019). - ISSN 0048-9697 - p. 1256 - 1265.
Aquatic ecosystems - Chemical pollution - Land use - Micropollutants - Multiple stressors - Pesticides

Water pollution is ubiquitous globally, yet how the effects of pollutants propagate through natural ecosystems remains poorly understood. This is because the interactive effects of multiple stressors are generally hard to predict. Agriculture and municipal wastewater treatment plants (WWTPs) are often major sources of contaminants for streams, but their relative importance and the role of different pollutants (e.g. nutrients or pesticides) are largely unknown. Using a ‘real world experiment’ with sampling locations up- and downstream of WWTPs, we studied how effluent discharges affected water quality and macroinvertebrate communities in 23 Swiss streams across a broad land-use gradient. Variation partitioning of community composition revealed that overall water quality explained approximately 30% of community variability, whereby nutrients and pesticides each independently explained 10% and 2%, respectively. Excluding oligochaetes (which were highly abundant downstream of the WWTPs) from the analyses, resulted in a relatively stronger influence (3%) of pesticides on the macroinvertebrate community composition, whereas nutrients had no influence. Generally, the macroinvertebrate community composition downstream of the WWTPs strongly reflected the upstream conditions, likely due to a combination of efficient treatment processes, environmental filtering and organismal dispersal. Wastewater impacts were most prominently by the Saprobic index, whereas the SPEAR index (a trait-based macroinvertebrate metrics reflecting sensitivity to pesticides) revealed a strong impact of arable cropping but only a weak impact of wastewater. Overall, our results indicate that agriculture can have a stronger impact on headwater stream macroinvertebrate communities than discharges from WWTP. Yet, effects of wastewater-born micropollutants were clearly quantifiable among all other influence factors. Improving our ability to further quantify the impacts of micropollutants requires highly-resolved water quality and taxonomic data with adequate spatial and temporal sampling. These improvements would help to better account for the underlying causal pathways that drive observed biological responses, such as episodic contaminant peaks and dispersal-related processes.

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.
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.
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.
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, Lisette de; Sawalha, Amr H. ; Direskeneli, Haner ; Saruhan-Direskeneli, Güher ; Guzeldemir-Akcakanat, Esra ; Keceli, 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. - \ 2017
Human Molecular Genetics 26 (2017)13. - ISSN 0964-6906 - p. 2577 - 2588.
Periodontitis is one of themost common inflammatory diseases, with a prevalence of 11% worldwide for the severe forms and an
estimated heritability of 50%. The disease is characterized by destruction of the alveolar bone due to an aberrant host
inflammatory response to a dysbiotic oral microbiome. Previous genome-wide association studies (GWAS) have reported several
suggestive susceptibility loci. Here, we conducted a GWAS using a German and Dutch case-control sample of aggressive periodontitis
(AgP, 896 cases, 7,104 controls), a rare but highly severe and early-onset form of periodontitis, validated the associations in a
German sample of severe forms of the more moderate phenotype chronic periodontitis (CP) (993 cases, 1,419 controls). Positive
findings were replicated in a Turkish sample of AgP (223 cases, 564 controls). A locus at SIGLEC5 (sialic acid binding Ig-like lectin 5)
and a chromosomal region downstream of the DEFA1A3 locus (defensin alpha 1-3) showed association with both disease phenotypes
and were associated with periodontitis at a genome-wide significance level in the pooled samples, with P¼1.09E-08
(rs4284742,-G; OR¼1.34, 95% CI¼1.21–1.48) and P¼5.48E-10 (rs2738058,-T; OR¼1.28, 95% CI¼1.18–1.38), respectively. SIGLEC5 is
expressed in various myeloid immune cells and classified as an inhibitory receptor with the potential tomediate tyrosine phosphatases
SHP-1/-2 dependent signaling. Alpha defensins are antimicrobial peptides with expression in neutrophils andmucosal
surfaces and a role in phagocyte-mediated host defense. This study identifies the first shared genetic risk loci of AgP and CP
with genome-wide significance and highlights the role of innate and adaptive immunity in the etiology of periodontitis.
Ethnobotanical knowledge of the Istro-Romanians of Zejane in Croatia
Pieroni, A. ; Giusti, M.E. ; Munz, H. ; Lenzarini, C. ; Turkovic, G. ; Turkovic, A. - \ 2003
Fitoterapia 74 (2003)39667. - ISSN 0367-326X - p. 710 - 719.
sempervivum-tectorum extract
An ethno-pharmacognostic survey was carried out in one of the smallest ethnic and linguistic groups in Europe: the Istro-Romanians of the village of Zejane (in Croatia), which has a population of approximately 140 persons, mainly elderly. Using an intensive field participant observation methodology, we recorded about 60 remedies of the local folk pharmacopoeia, and mainly derived from plants. Among them, the uncommon traditions to use homemade vinegar from wild apple (Malus sylvestris) and Cornelian cherries (Cornus mas) for diverse medical purposes, and houseleek (Sempervivum tectorum) against ear pains have been briefly discussed
Gender issues in agriculture: lessons from sub-saharan African countries.
Safilios-Rothschild, C. - \ 1991
In: Towards a new agrarian democratic order: beyond apartheid. Reader on the South African land question / Matlhape, S., Münz, A., - p. 281 - 285.
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