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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    de Toekomst van Natuur en Energie in Nederland
    Hattum, Tim van; Rooij, Bertram de - \ 2020

    de Toekomst van Natuur en Energie in Nederland n.a.v. Kaart NL2120, interview van Marlies Dekkers met Tim van Hattum en Bertram de Rooij

    Identification and in silico bioinformatics analysis of PR10 proteins in cashew nut
    Bastiaan-Net, Shanna ; Pina-Pérez, Maria C. ; Dekkers, Bas J.W. ; Westphal, Adrie H. ; America, Antoine H.P. ; Ariëns, Renata M.C. ; Jong, Nicolette W. de; Wichers, Harry J. ; Mes, Jurriaan J. - \ 2020
    Protein Science 29 (2020)7. - ISSN 0961-8368 - p. 1581 - 1595.
    Anacardium occidentale - Bet v 1-like - cashew nut - in silico allergenicity analysis - oral allergy syndrome (OAS) - PR10 - RNA-seq

    Proteins from cashew nut can elicit mild to severe allergic reactions. Three allergenic proteins have already been identified, and it is expected that additional allergens are present in cashew nut. pathogenesis-related protein 10 (PR10) allergens from pollen have been found to elicit similar allergic reactions as those from nuts and seeds. Therefore, we investigated the presence of PR10 genes in cashew nut. Using RNA-seq analysis, we were able to identify several PR10-like transcripts in cashew nut and clone six putative PR10 genes. In addition, PR10 protein expression in raw cashew nuts was confirmed by immunoblotting and liquid chromatography–mass spectrometry (LC–MS/MS) analyses. An in silico allergenicity assessment suggested that all identified cashew PR10 proteins are potentially allergenic and may represent three different isoallergens.

    Process history of calcium caseinate affects fibre formation
    Wang, Zhaojun ; Dekkers, Birgit L. ; Goot, Atze Jan van der - \ 2020
    Journal of Food Engineering 275 (2020). - ISSN 0260-8774
    Calcium caseinate - Drying - Fibre - Mechanical properties - Roller - Spray drying - Thermal history

    In this study, we compared the physical properties and structuring potential of spray-dried calcium caseinate (Scaca) and roller-dried calcium caseinate (Rcaca). Scaca formed more pronounced fibrous materials upon shearing compared with Rcaca. The rheological measurements revealed that the Scaca dispersion exhibited more solid-like behaviour. Besides, the particle size in excess water was larger for Rcaca (2–300 μm), while Scaca mainly contained small caseinate aggregates (<800 nm). Finally, Rcaca was less susceptible to enzymatic crosslinking with transglutaminase. The different physical properties and structuring potentials were explained by the intensive thermal treatment during roller drying for Rcaca. The application of a similar thermal process to Scaca resulted in similar properties as Rcaca. We concluded that the process history of calcium caseinate has major consequences for its fibre formation potential.

    GSE's 50th anniversary : Where do we go from now?
    Boichard, Didier ; Dekkers, Jack ; Hayes, Helene ; Werf, Julius van der; Bovenhuis, Henk ; Calus, Mario ; Groenen, Martien - \ 2019
    Genetics, Selection, Evolution 51 (2019). - ISSN 0999-193X
    Toasting as a tool to improve the functional properties of fababean protein concentrate
    Bühler, J. ; Dekkers, B.L. ; Bruins, M.E. ; Goot, A.J. van der - \ 2019
    Wageningen University & Research - 1 p.
    Toasting as a tool - protein concentration
    Protein Oxidation and in Vitro Gastric Digestion of Processed Soy-Based Matrices
    Duque-Estrada, Patrícia ; Berton-Carabin, Claire C. ; Nieuwkoop, Matthijs ; Dekkers, Birgit L. ; Janssen, Anja E.M. ; Goot, Atze Jan Van Der - \ 2019
    Journal of Agricultural and Food Chemistry 64 (2019)34. - ISSN 0021-8561 - p. 9591 - 9600.
    gastric digestion - meat analogues - processing - protein oxidation - soy proteins

    Process conditions that are applied to make structured soy-protein-based food commonly include high temperatures. Those conditions can induce protein oxidation, leading to a decrease in their susceptibility to proteolysis by digestive enzymes. We aimed to investigate the effects of thermomechanical processing on oxidation and in vitro gastric digestion of commercial soy protein ingredients. Samples were sheared at 100 to 140 °C and characterized for acid uptake, carbonyl content, electrophoresis, and surface hydrophobicity. The enzymatic hydrolysis was determined in simulated gastric conditions. Protein ingredients were already oxidized and showed higher surface hydrophobicity and hydrolysis rate compared with those of the processed matrices. However, no clear correlation between the level of carbonyls and the hydrolysis rate was found. Therefore, we conclude that gastric digestion is mostly driven by the matrix structure and composition and the available contact area between the substrate and proteolytic enzymes.

    DELAY OF GERMINATION 1-LIKE 4 acts as an inducer of seed reserve accumulation
    Sall, Khadidiatou ; Dekkers, Bas J.W. ; Nonogaki, Mariko ; Katsuragawa, Yoshihiko ; Koyari, Ryosuke ; Hendrix, David ; Willems, Leo A.J. ; Bentsink, Leónie ; Nonogaki, Hiroyuki - \ 2019
    The Plant Journal 100 (2019)1. - ISSN 0960-7412 - p. 7 - 19.
    abscisic acid - dormancy - hormone - seed development - seed maturation - storage proteins

    More than 70% of global food supply depends on seeds. The major seed reserves, such as proteins, lipids, and polysaccharides, are produced during seed maturation. Here, we report that DELAY OF GERMINATION 1-LIKE 4 (DOGL4) is a major inducer of reserve accumulation during seed maturation. The DOGL family proteins are plant-specific proteins of largely unknown biochemical function. DOGL4 shares only limited homology in amino acid sequence with DOG1, a major regulator of seed dormancy. DOGL4 was identified as one of the outstanding abscisic acid (ABA)-induced genes in our RNA sequencing analysis, whereas DOG1 was not induced by ABA. Induction of DOGL4 caused the expression of 70 seed maturation-specific genes, even in germinating seeds, including the major seed reserves ALBUMIN, CRUCIFERIN and OLEOSIN. Although DOG1 affects the expression of many seed maturation genes, the major seed reserve genes induced by DOGL4 are not altered by the dog1 mutation. Furthermore, the reduced dormancy and longevity phenotypes observed in the dog1 seeds were not observed in the dogl4 mutants, suggesting that these two genes have limited functional overlap. Taken together, these results suggest that DOGL4 is a central factor mediating reserve accumulation in seeds, and that the two DOG1 family proteins have diverged over the course of evolution into independent regulators of seed maturation, but retain some overlapping function.

    Mug en daas in Baronie worden aangepakt
    Verdonschot, P.F.M. ; Dekkers, T.B.M. - \ 2019
    Met kennis de markt op
    Dekkers, B.L. ; Kortekaas, J.A. ; Meiling, Jan ; Houthoff, Iris ; Goot, A.J. van der; Berendse, Sebastiaan - \ 2019
    Marketing knowledge
    Kortekaas, J.A. ; Meiling, Jan ; Goot, A.J. van der; Dekkers, B.L. ; Houthoff, Iris ; Wijffels, R.H. ; Lindner, F. - \ 2019

    Researchers and students are increasingly being challenged to think about how they can market their knowledge. Various startups and spin-offs are already under development. ‘We no longer wait until an enterprising researcher wants to go into business.’

    Comparing structuring potential of pea and soy protein with gluten for meat analogue preparation
    Schreuders, Floor K.G. ; Dekkers, Birgit L. ; Bodnár, Igor ; Erni, Philipp ; Boom, Remko M. ; Goot, Atze Jan van der - \ 2019
    Journal of Food Engineering 261 (2019). - ISSN 0260-8774 - p. 32 - 39.
    Fibrous structures - Food processing - Plant protein - Shear cell processing - Shear-induced structuring

    Pea protein isolate can be combined with wheat gluten into materials with a fibrous morphology using shear induced structuring combined with heating. Results are partly in-line with soy protein isolate-wheat gluten blends, but the latter yields anisotropic materials in a much broader temperature range. Both blends also have the ability to include air. Air bubbles were aligned and deformed at process conditions that gave the most pronounce fibrous products. Mechanically, the pea protein-gluten materials processed at 140 °C had a similar strength as soy protein blends. At 110 and 120 °C, the pea protein blends had a strength that was comparable to a chicken meat reference (50–100 kPa) but weaker than their counterparts with soy (220–300 kPa). Blends of pea protein-gluten show potential for preparing structured plant protein materials, but the application area might be different compared with potential applications of soy protein-gluten blends.

    Maltodextrin promotes calcium caseinate fibre formation through air inclusion
    Wang, Zhaojun ; Dekkers, Birgit L. ; Boom, Remko ; Goot, Atze Jan van der - \ 2019
    Food Hydrocolloids 95 (2019). - ISSN 0268-005X - p. 143 - 151.
    Air bubble - Anisotropy - Calcium caseinate - Fibrous appearance - Maltodextrin

    Commercial calcium caseinate is available as spray-dried and roller-dried powder. Shearing a dense spray-dried calcium caseinate dispersion gives rise to a fibrous material, whereas shearing dense roller-dried calcium caseinate yields a layered material with only slight anisotropy in mechanical strength. The addition of a polysaccharide phase in a continuous protein phase may lead to formation of fibrous structures after shearing, which is hypothesized to be a result of the elongation and orientation of the dispersed polysaccharide domains. We report the effect of the addition of maltodextrin to roller-dried calcium caseinate on structure formation. The strength of the material increased with the addition of maltodextrin, which is partly caused by the withdrawal of water from the caseinate phase towards the maltodextrin phase, leading to a higher local caseinate concentration. The anisotropy of fracture stress and fracture strain were enhanced with up to 5 wt% maltodextrin. The effect of maltodextrin on the mechanical anisotropy and fibrous appearance could be ascribed to the greater air incorporation as a result of the presence of maltodextrin.

    Towards a sustainable banana supply chain in Colombia : Rainforest Alliance Certification and economic, social and environment conditions on small-scale banana plantations in Magdalena, Colombia
    Beekman, G. ; Dekkers, M. ; Koster, T. - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2019-019) - ISBN 9789463435581 - 48
    De bodemfauna van het Markermeer : Markermeer bodemfaunakartering 2016 en MWTL-analyse
    Riel, M.C. van; Verdonschot, P.F.M. ; Dekkers, D.D. - \ 2018
    Wageningen : Zoetwaterecosystemen, Wageningen Environmental Research (Notitie Zoetwatersystemen, Wageningen Environmental Research ) - ISBN 9789463437516 - 48
    Software Development for Deterministic Prediction of Selection Response in Livestock Breeding Programs Using Genomic Information
    Su, H. ; Bijma, P. ; Werf, Julius van der; Dekkers, J.C.M. - \ 2018
    Journal of Animal Science 96 (2018)Supplement 2. - ISSN 0021-8812 - p. 19 - 19.
    Theory to predict selection response in traditional livestock breeding programs has been well developed, validated and implemented in software in the past decades, for example in SelAction (Rutten et al. 2002), which has been successful as a tool to predict selection response in traditional livestock breeding programs for a wide range of population structures and selection strategies. This software used standard quantitative genetics theory and selection index theory to develop deterministic recursive equations, which model changes of trait means and variance-covariance structures to predict asymptotic response to multiple trait selection using best linear unbiased prediction (BLUP) estimated breeding values (EBV). Nowadays genetic improvement can further be enhanced by genomic predictions, which provide more accurate estimates of breeding values of animals in their earlier life and can improve the efficiency of breeding programs. While statistical methods to estimate genomic breeding values are now widely available, optimizing the use of genomics in practical livestock breeding programs is limited due to the lack of computer software that implements available theories. We're hereby to present a computer program that extends SelAction. Genomic information is included as the average phenotype of groups of individuals with both genotypic and phenotypic information following Wientjes et al. (2016). The heterogeneity of genomic information is considered in terms of the degree of relationship between selection candidates and the individuals that are both genotyped and phenotyped (van der Werf et al., 2015). This software can be used by breeders to reliably compare alternative breeding programs and for investment decisions for breeding programs that include genomic information.
    Plant-Based Meat Analogues
    Kyriakopoulou, K. ; Dekkers, B.L. ; Goot, A.J. van der - \ 2018
    In: Sustainable Meat Production and Processing / Galanakis, Charis, Academic Press - ISBN 9780128148747 - p. 103 - 126.
    As the world's population increases, the need for reliable protein sources is growing. Meat is considered a good source of high biological value protein, but meat is not sustainable. In Western countries, the shift toward a diet with reduced meat consumption demands healthy and tasteful meat-free food products. Following this trend, the market turned toward vegetable proteins, such as pulses, wheat gluten and soy protein, which are processed into meat-like products, also known as meat analogues. These products approximate certain aesthetic qualities, such as texture, flavor, and color, and nutritional characteristics of specific types of meat. The development of new, attractive food products is a challenge already, but this challenge becomes even greater considering that these products are meant as a substitute for meat. This chapter discusses the insights concerning plant-based meat analogues, their production and future developments.
    Harnessing longitudinal information to identify genetic variation in tolerance of pigs to Porcine Reproductive and Respiratory Syndrome virus infection
    Lough, Graham ; Hess, Andrew ; Hess, Melanie ; Rashidi, Hamed ; Matika, Oswald ; Lunney, Joan K. ; Rowland, Raymond R.R. ; Kyriazakis, Ilias ; Mulder, Han A. ; Dekkers, Jack C.M. ; Doeschl-Wilson, Andrea - \ 2018
    Genetics, Selection, Evolution 50 (2018). - ISSN 0999-193X

    Background: High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are resilient to infections. For Porcine Reproductive and Respiratory Syndrome (PRRS), one of the most devastating swine diseases worldwide, studies have identified substantial genetic variation in resistance of pigs, but evidence for genetic variation in tolerance has so far been inconclusive. Resistance and tolerance are usually considered as static traits. In this study, we used longitudinal viremia measurements of PRRS virus infected pigs to define discrete stages of infection based on viremia profile characteristics. These were used to investigate host genetic effects on viral load (VL) and growth at different stages of infection, to quantify genetic variation in tolerance at these stages and throughout the entire 42-day observation period, and to assess whether the single nucleotide polymorphism (SNP) WUR10000125 (WUR) with known large effects on resistance confers significant differences in tolerance. Results: Genetic correlations between resistance and growth changed considerably over time. Individuals that expressed high genetic resistance early in infection tended to grow slower during that time-period, but were more likely to experience lower VL and recovery in growth by the later stage. The WUR genotype was most strongly associated with VL at early- to mid-stages of infection, and with growth at mid- to late-stages of infection. Both, single-stage and repeated measurements random regression models identified significant genetic variation in tolerance. The WUR SNP was significantly associated only with the overall tolerance slope fitted through all stages of infection, with the genetically more resistant AB pigs for the WUR SNP being also more tolerant to PRRS. Conclusions: The results suggest that genetic selection for improved tolerance of pigs to PRRS is possible in principle, but may be feasible only with genomic selection, requiring intense recording schemes that involve repeated measurements to reliably estimate genetic effects. In the absence of such records, consideration of the WUR genotype in current selection schemes appears to be a promising strategy to improve simultaneously resistance and tolerance of growing pigs to PRRS.

    Structuring processes for meat analogues
    Dekkers, Birgit L. ; Boom, Remko M. ; Goot, Atze Jan van der - \ 2018
    Trends in Food Science and Technology 81 (2018). - ISSN 0924-2244 - p. 25 - 36.
    Anisotropy - Fibrous products - Meat analogues - Plant protein - Structuring

    Background: Animal-derived protein foods, such as meat, have a large impact on the environment. Meat analogues are products that replace meat in its functionality, i.e. have similar product properties and sensory attributes, which is achieved by the fibrous nature of those products. Scope and approach: The techniques used to make fibrous products that mimic muscle meats are outlined and categorized based on their approach. The bottom-up approach refers to assembly of structural elements that are combined. The top-down approach refers to structuring of biopolymer blends using an overall force field. The strengths and weaknesses of these approaches are discussed in terms of ingredient and equipment use, (achievable) product resemblance, robustness, scalability, and resource efficiency. To enlarge the theoretical framework, the techniques with the top-down strategy are further contextualized by relating to structure formation processes of materials with other applications, and the methods to analyse the fibrous structures are further outlined. Key findings and conclusions: Techniques that follow the bottom-up strategy have the potential to resemble the structure of meat most closely, by structuring the proteins hierarchically through assembly of individual structural components. The top-down strategy is better scalable, is more efficient in its use of resources, but can only create the desired structure on larger length scales. Significant progress has been made on the methods to analyse structured products from the last category. Most analysis methods focussed on the (micro)structural anisotropy of the fibrous products, however there is also a need for methods that allow in situ analysis of the evolution of the structure during processing.

    Creation of fibrous plant protein foods
    Dekkers, Birgit L. - \ 2018
    Wageningen University. Promotor(en): A.J. van der Goot; R.M. Boom. - Wageningen : Wageningen University - ISBN 9789463433198 - 204
    cum laude

    A transition from animal to plant-based protein is required to produce sufficient protein for the growing world population, while at the same time mitigates climate change. Especially the production of meat imposes a burden on the environment. Meat analogues, which are products that are similar to meat in its functionality, can help consumers to lower their meat consumption. The anisotropic, fibrous nature of meat is perhaps the most important characteristic of meat, which can be mimicked by structuring biopolymers, such as proteins and polysaccharides with the shear cell technology. The aim of this thesis is to obtain insight in the key mechanisms that play a role in the transformation of plant-based biopolymer blends into anisotropic/fibrous structures with shear cell technology. These two key mechanisms are the deformation of the two phases present in biopolymer blends, and the subsequent entrapment of this deformation during solidification. It was concluded that successful structure formation requires matching of the properties of the two phases. During structuring at elevated temperature, the two phases are deformed, while subsequent cooling ensures entrapment of the deformed dispersed phase(s) in the (continuous) phase. Ideally, the continuous and dispersed phase have different strength in the final product,.

    Chapter 2 presents a method to determine the water distribution in soy protein isolate (SPI) – wheat gluten (WG) blends. The concentration of water in each separate phase was directly determined with time-domain nuclear magnetic resonance relaxometry (TD-NMR), and oscillatory rheology was used to indirectly asses the water distribution by determining the viscoelastic properties of the separate phases and the blend. It was shown that water distributes unevenly in SPI-WG blends: more water was absorbed by the SPI as compared to the WG phase. This methodology was developed for SPI-WG blends at room temperature and subsequently also applied to heated and sheared samples in Chapter 3. First, water distribution in the blend after a heat and/or shear treatment was assessed with TD-NMR and the outcomes were then used to predict the viscoelastic properties of the SPI and WG phase in the blend. This yielded insight in the deformability of the two phases in the blend. The viscoelastic properties were measured under conditions that are relevant for structure formation, i.e. during and after heating and shearing. It was shown that the water distribution was hardly affected by a heat or shear treatment, whereas the viscoelastic properties of the two phases changed significantly. The viscoelastic properties of SPI and WG became more similar due to water redistribution in the blend, which allows deformation and alignment of the dispersed phase during structuring.

    Chapter 4 describes a study using a model blend that mimics soy protein concentrate (SPC). It consists of a relatively pure protein phase, soy protein isolate (SPI), and a soluble, more or less pure polysaccharide phase, pectin. This SPI-pectin blend formed fibrous materials at a similar heating temperature as SPC, being 140°C. Pectin formed the dispersed phase and was deformed when heated and sheared at optimal conditions. Chapter 5 extends the study on structure formation with SPI-pectin blends. Here, the deformation of the dispersed pectin phase and the influence of incorporated air were considered. The fibrous nature of these products appears upon tearing, and originates from detachment through or along the long side of the weak dispersed phase(s), being pectin and/or air. A model based on the rule of mixing was used to predict the mechanical anisotropy based on the volume fraction and the deformation of the weak, dispersed phase. The size and orientation of the dispersed phases, tailored by using different shear rates, were related to differences in fracture behavior when deforming the structures. Besides deformation, the strength and volume fraction of the weak phase(s) were important when composing a blend for fibrous structure formation. In Chapter 6, the behavior of the SPI and pectin phases in a blend was investigated by determining the viscoelastic properties while shearing and heating over time. A closed cavity rheometer (CCR) was used to determine these properties under similar conditions as used during fibrous structure formation. The addition of a small amount of pectin (2.2 wt.%) to a SPI dispersion (41.8 wt.%) resulted in viscoelastic behavior that changed in time during a shear treatment at elevated temperatures. Although one can clearly discern two distinct phases with SEM, the viscoelastic behavior of the SPI-pectin blend is more complex than that of a simple composite material.

    Chapter 7 demonstrates the importance of the fractionation process on the structuring potential of soy proteins. An enriched soy protein fraction was obtained through an aqueous fractionation process. Those fractions could be used to make fibrous structures when: i) the soy protein fractions were toasted, which is a dry heating step, and ii) when a concentrate (75% protein) was combined with full fat flour, in such a ratio that the protein content was similar to commercial SPC. Toasting results in decreased protein solubility, increased water holding capacity and increased viscosity of the fractions, and these changes turned out to be important for fibrous structure formation.

    Lastly, literature was reviewed to put all findings in perspective (Chapter 8). An overview is presented of all techniques that are commercially used and currently investigated to create meat-like structures. Structuring techniques are compared in their approach, being either bottom-up, which refers to assembly of structural elements that are then combined, or top-down, which refers to structuring of biopolymer blends using an overall force field. A bottom-up strategy has the potential to resemble the structure of meat most closely, by structuring the molecules including proteins into structural components (e.g. muscle cells) followed by assembly of individual structural components. A top-down strategy is more efficient in its use of resources and is better scalable, but can only create the desired structure on larger length scales. The techniques with a top-down strategy were further investigated by reviewing literature on similar processes outside this particular field of application, i.e. not meant to create fibrous structures. These insights were subsequently translated to the conditions as used in structure formation for meat analogues.

    Chapter 9 concludes with a general discussion of all results presented in this thesis. The different chapters are integrated in design rules for fibrous structure formation. Furthermore, the complexity encountered when studying material and conditions during fibrous structure formation are discussed. Then, the potential and the challenges for understanding and applying fibrous structure formation with simple shear flow are summarized.

    The overall societal goal of developing meat analogue food products is to help consumers in the transition from animal-based to a more plant-based diet. The scientific goal to obtain insight in fibrous structure formation with the shear technology as developed in this thesis is of importance, and can be the basis for developing the technology for the next generation meat analogues.

    Towards sustainable cocoa in Côte d'Ivoire : The impacts and contribution of UTZ certification combined with services provided by companies
    Ingram, V. ; Rijn, F. van; Waarts, Y. ; Dekkers, M. ; Vos, B. de; Koster, T. ; Tanoh, R. ; Galo, A. - \ 2018
    Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2018-041) - ISBN 9789463437769 - 137
    Stekende insecten Griendtsveen 2017 : notitie
    Verdonschot, Piet F.M. ; Dekkers, T.B.M. - \ 2018
    Wageningen : Zoetwaterecosystemen, Wageningen Environmental Research - ISBN 9789463432924 - 58
    De inventarisatie van steekmuglarven leverde in 2016 4 kleinere gebiedsdelen op met hoge aantallen steekmuglarven (de zogenaamde ‘hotspots’). In april-mei 2017 is de larveninventarisatie herhaald. Hieruit bleek dat de larven van de moerassteekmug A. cinereus over het gehele gebied verspreid zijn met op de ‘hotspots’ opnieuw hoogste aantallen. In de periode daarna vielen de meeste locaties droog. Het jaar 2017 was een droog jaar waarbij al vroeg in het voorjaar, mogelijk zelfs in de winter, veel potentiële tijdelijke wateren al droog stonden. Het patroon van ontwikkeling van volwassen steekmuggen liet over 2017 een ‘klassiek’ beeld van een moerassteekmuggenpopulatie zien met hoge aantallen in het voorjaar die daarna snel uitdoven. Alleen in juni trad additioneel een kleine populatie van plantenboorsteekmuggen op. Dit beeld is een gevolg van het opdrogen van tijdelijke wateren in het gebied in het voorjaar. De in totaal lagere aantallen in het gehele gebied en de beperking van deze aantallen tot de maand mei hebben ertoe geleid dat in het dorp Griendtsveen in 2017 geen overlast is ervaren. De verdeling van de aantallen over de jaren 2015, 2016 en 2017 naar zone rondom en in het dorp laat zien dat er ieder jaar een afname van de aantallen optreedt richting de dorpskern. In de periode 2015-2017 is het aantallen verzamelde knutten toegenomen met een factor 3. Dit kan samenhangen met nattere weilanden aan de zuidzijde, in het dorp en aan de westzijde. De adviezen voor maatregelen om de ‘hotspots’ aan te pakken zijn in 2017 in gang gezet en ten dele uitgevoerd
    DNA methylation as a mediator of the association between prenatal adversity and risk factors for metabolic disease in adulthood
    Tobi, Elmar W. ; Slieker, Roderick C. ; Luijk, René ; Dekkers, Koen F. ; Stein, Aryeh D. ; Xu, Kate M. ; Slagboom, P.E. ; Zwet, Erik W. Van; Lumey, L.H. ; Heijmans, Bastiaan T. ; T'Hoen, Peter A. ; Pool, René ; Greevenbroek, Marleen M. Van; Stehouwer, Coen D. ; Kallen, Carla J. Van Der; Schalkwijk, Casper G. ; Wijmenga, Cisca ; Zhernakova, Sasha ; Tigchelaar, Ettje F. ; Beekman, Marian ; Deelen, Joris ; Heemst, Diana Van; Veldink, Jan H. ; Berg, Leonard H. Van Den; Duijn, Cornelia M. Van; Hofman, Albert ; Uitterlinden, André G. ; Jhamai, P.M. ; Verbiest, Michael ; Verkerk, Marijn ; Breggen, Ruud Van Der; Rooij, Jeroen Van; Lakenberg, Nico ; Mei, Hailiang ; Bot, Jan ; Zhernakova, Dasha V. ; Hof, Peter Van 't; Deelen, Patrick ; Nooren, Irene ; Moed, Matthijs ; Vermaat, Martijn ; Jan Bonder, Marc ; Dijk, Freerk Van; Arindrarto, Wibowo ; Kielbasa, Szymon M. ; Swertz, Morris A. ; Isaacs, Aaron ; Franke, Lude - \ 2018
    Science Advances 4 (2018)1. - ISSN 2375-2548
    Although it is assumed that epigenetic mechanisms, such as changes in DNA methylation (DNAm), underlie the relationship between adverse intrauterine conditions and adult metabolic health, evidence from human studies remains scarce. Therefore, we evaluated whether DNAm in whole blood mediated the association between prenatal famine exposure and metabolic health in 422 individuals exposed to famine in utero and 463 (sibling) controls. We implemented a two-step analysis, namely, a genome-wide exploration across 342, 596 cytosine-phosphate-guanine dinucleotides (CpGs) for potential mediators of the association between prenatal famine exposure and adult body mass index (BMI), serum triglycerides (TG), or glucose concentrations, which was followed by formalmediation analysis.DNAm mediated the association of prenatal famine exposure with adult BMI and TG but not with glucose. DNAm at PIM3 (cg09349128), a gene involved in energy metabolism, mediated 13.4% [95% confidence interval (CI), 5 to 28%] of the association between famine exposure and BMI. DNAm at six CpGs, including TXNIP (cg19693031), influencing b cell function, and ABCG1 (cg07397296), affecting lipid metabolism, together mediated 80% (95% CI, 38.5 to 100%) of the association between famine exposure and TG. Analyses restricted to those exposed to famine during early gestation identified additional CpGs mediating the relationship with TG near PFKFB3 (glycolysis) and METTL8 (adipogenesis). DNAm at the CpGs involved was associated with gene expression in an external data set and correlated with DNAm levels in fat depots in additional postmortem data. Our data are consistent with the hypothesis that epigenetic mechanisms mediate the influence of transient adverse environmental factors in early life on long-termmetabolic health. The specific mechanism awaits elucidation.
    Viscoelastic properties of soy protein isolate - pectin blends: Richer than those of a simple composite material
    Dekkers, B.L. ; Boom, R.M. ; Goot, A.J. van der - \ 2018
    Food Research International 107 (2018). - ISSN 0963-9969 - p. 281 - 288.
    Concentrated soy protein isolate (SPI) – pectin blends acquire fibrous textures by shear-induced structuring while heating. The objective of this study was to determine the viscoelastic properties of concentrated SPI-pectin blends under similar conditions as during shear-induced structuring, and after cooling. A closed cavity rheometer was used to measure these properties under these conditions. At 140 °C, SPI and pectin had both a lower G* than the blend of the two and also showed a different behavior in time. Hence, the viscoelastic properties of the blend are richer than those of a simple composite material with stable physical phase properties. In addition, the G′pectin was much lower compared with the G′SPI and G′SPI-pectin upon cooling, confirming that pectin formed a weak dispersed phase. The results can be explained by considering that the viscoelastic properties of the blend are influenced by thermal degradation of the pectin phase. This degradation leads to: i) release of galacturonic acid, ii) lowering of the pH, and iii) water redistribution from the SPI towards the pectin phase. The relative importance of those effects are evaluated.
    Metabolic imaging of fatty kidney in diabesity : Validation and dietary intervention
    Jonker, Jacqueline T. ; Heer, Paul De; Engelse, Marten A. ; Rossenberg, Evelien H. Van; Klessens, Celine Q.F. ; Baelde, Hans J. ; Bajema, Ingeborg M. ; Koopmans, Sietse Jan ; Coelho, Paulo G. ; Streefland, Trea C.M. ; Webb, Andrew G. ; Dekkers, Ilona A. ; Rabelink, Ton J. ; Rensen, Patrick C.N. ; Lamb, Hildo J. ; Vries, Aiko P.J. De - \ 2018
    Nephrology Dialysis Transplantation 33 (2018)2. - ISSN 0931-0509 - p. 224 - 230.
    chronic kidney disease - fatty kidney - proton magnetic - renal triglyceride content - resonance spectroscopy - type 2 diabetes mellitus
    Background Obesity and type 2 diabetes have not only been linked to fatty liver, but also to fatty kidney and chronic kidney disease. Since non-invasive tools are lacking to study fatty kidney in clinical studies, we explored agreement between proton magnetic resonance spectroscopy (1 H-MRS) and enzymatic assessment of renal triglyceride content (without and with dietary intervention). We further studied the correlation between fatty kidney and fatty liver. Methods Triglyceride content in the renal cortex was measured by 1 H-MRS on a 7-Tesla scanner in 27 pigs, among which 15 minipigs had been randomized to a 7-month control diet, cafeteria diet (CAF) or CAF with low-dose streptozocin (CAF-S) to induce insulin-independent diabetes. Renal biopsies were taken from corresponding MRS-voxel locations. Additionally, liver biopsies were taken and triglyceride content in all biopsies was measured by enzymatic assay. Results Renal triglyceride content measured by 1 H-MRS and enzymatic assay correlated positively (r = 0.86, P < 0.0001). Compared with control diet-fed minipigs, renal triglyceride content was higher in CAF-S-fed minipigs (137 ± 51 nmol/mg protein, mean ± standard error of the mean, P < 0.05), but not in CAF-fed minipigs (60 ± 10 nmol/mg protein) compared with controls (40 ± 6 nmol/mg protein). Triglyceride contents in liver and kidney biopsies were strongly correlated (r = 0.97, P < 0.001). Conclusions Non-invasive measurement of renal triglyceride content by 1 H-MRS closely predicts triglyceride content as measured enzymatically in biopsies, and fatty kidney appears to develop parallel to fatty liver. 1 H-MRS may be a valuable tool to explore the role of fatty kidney in obesity and type 2 diabetic nephropathy in humans in vivo.
    Novel processing concepts for making fibrous food products
    Dekkers, B.L. ; Goot, A.J. van der - \ 2018
    In: Intensification of Biobased Processes / Górak, Andrzej, Stankiewicz, Andrzej, Royal Society of Chemistry (RSC Green Chemistry 55) - ISBN 9781782628552 - p. 462 - 477.
    A route to make Western diets more sustainable is through reduction of the consumption of animal-derived products. The simplest route to achieve this is to replace animal-derived products with vegetables, beans or pulses. However, modern consumers highly appreciate the texture and juiciness of meat. That is why scientists and food engineers aim to mimic the structure of meat using plant-derived ingredients. In this book chapter, we describe the need to reduce meat consumption in more detail and outline current processes to make today's meat analog products. However, the current products do not satisfy all consumer demands with respect to taste, texture and/or price. That is why we present novel routes and processing concepts currently being studied to make meat analogs. Those routes include concepts that aim to rebuild structures using molecular orientation, cellular imitation and methods that aim to alter naturally present structures in plant materials. The chapter ends by reviewing possible raw materials to be used in those applications and the importance of understanding the effect on functional properties when preparing the ingredients.
    The phase properties of soy protein and wheat gluten in a blend for fibrous structure formation
    Dekkers, B.L. ; Azad Emin, M. ; Boom, R.M. ; Goot, A.J. van der - \ 2018
    Food Hydrocolloids 79 (2018). - ISSN 0268-005X - p. 273 - 281.
    Fibrous macrostructures can be obtained from among others soy protein isolate (SPI) - wheat gluten (WG) blends, when deformed with simple shear flow while heating. This SPI-WG blend consists of two phases, which are separated on a micrometer scale. The properties, especially the rheological properties, of SPI- andWG-phases determine the structure formation process largely. The objective of this study was to determine the properties of the phases present in SPI-WG blends using conditions relevant for fibrous structure formation. Since, the rheological properties are dependent on the concentration of each protein
    in its respective phase, we determined the water content in the two phases with a methodology based on time-domain nuclear magnetic resonance. The spatial distribution of the two phases was studied with confocal scanning laser microscopy, and the rheological properties were measured with three types of
    oscillatory rheology. The experiments showed that the SPI-phase absorbed more water than the WGphase, which resulted in a larger volume fraction than mass fraction of the SPI-phase and vice versa for WG. The absorption of more water by SPI resulted in a lower concentration of SPI in that phase, remarkably leading to a G0-value for SPI that was similar to the rheological properties of WG. Similarities
    in rheological properties seem to be required to strongly deform and align the dispersed phase and form fibrous macrostructures.
    Aqueous fractionation processes of soy protein for fibrous structure formation
    Geerts, Marlies E.J. ; Dekkers, Birgit L. ; Padt, Albert van der; Goot, Atze Jan van der - \ 2018
    Innovative Food Science and Emerging Technologies 45 (2018). - ISSN 1466-8564 - p. 313 - 319.
    Desired properties of ingredients differ for various applications. Here, we use a reverse engineering approach to obtain soy protein fractions targeted for the application of meat analogs. Aqueous fractionation was used to produce these soy protein fractions, which were structured with simple shear flow deformation while heating. The water holding capacity (WHC), nitrogen solubility index (NSI), enthalpy of transition, and viscoelastic properties were determined. We found that a soy protein fraction/full fat flour blend resulted in distinct fibrous structures but only when the soy protein fraction was toasted at 150 °C. At this optimum toasting temperature (150 °C), the protein fractions had a high WHC, intermediate NSI and its viscoelastic property was characterized as G* between 1 and 10 kPa. These functional properties were shown to be key for fibrous structure formation, whereas, the influence of the state of the proteins was limited. Industrial relevance The market for meat analogs is growing. Nowadays, most of the meat analogs are produced with soy protein concentrates and isolates. These concentrates and isolates are obtained with conventional fractionation processes that involve organic solvents to extract the oil first. As a result, the application of these ingredients is limited, e.g. the product cannot be classified as organic. In this study, we therefore investigated aqueous fractionation of soy to obtain a soy protein fraction with desired functionality that can be used for the application of meat analogs and satisfy the values of consumers.
    Understanding fiber formation in a concentrated soy protein isolate - Pectin blend
    Dekkers, Birgit L. ; Hamoen, Remco ; Boom, Remko M. ; Goot, Atze Jan van der - \ 2018
    Journal of Food Engineering 222 (2018). - ISSN 0260-8774 - p. 84 - 92.
    Droplet breakup - Droplet coalescence - Mechanical properties - Microstructure - Shear-induced deformation - Water-in-water emulsion
    Concentrated blends of pectin in soy protein, subjected to simple shear flow while heated form solid, fibrous materials that are a basis for meat analogues. The commonly accepted ‘rule of mixing’ based on the cross-sectional area of a weak dispersed phase was used to predict mechanical anisotropy of the material. Experimentally, two different dispersed phases were observed in the continuous soy protein matrix; air and pectin. An optimum in shape anisotropy of the air and pectin droplets, and mechanical anisotropy was found for a shear rate of 39 s−1. At higher shear rates, air was expelled and break-up of pectin droplets was found, resulting in materials with hardly any mechanical anisotropy. There was discrepancy between the modeled and experimental data when using the same mass fraction and volume fraction of pectin, whereas the model fitted better when assuming that the pectin phase absorbs more water relatively to the soy phase.
    The phase behaviour of soy protein and wheat gluten blends used for fibrous structure formation
    Dekkers, Birgit - \ 2017
    Klimaatverandering in de Grote Polder en Polder Groenendijk : Workshopverslag
    Goosen, H. ; Rooij, L.L. de; Steingröver, E.G. ; Opdam, P.F.M. ; Haan, E. de; Dekkers, F. - \ 2017
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport ) - 18
    Het klimaat verandert en dat merken we langzaam maar zeker. Maar wat zijn hiervan de gevolgen op lokaal niveau? Om hier een beeld van te vormen is informatie over klimaatverandering en (land)gebruik samengebracht voor de Grote Polder en Polder Groenendijk. Kunnen we een eerste beeld vormen van wat klimaatverandering betekent voor het bedrijfsleven op het bedrijvenpark, voor de Heineken-brouwerij, voor de gemeente Zoeterwoude, voor het Hoogheemraadschap van Rijnland, voor de boeren, voor de natuur, en voor de mensen die er wonen en recreëren? Tijdens een bijeenkomst op 28 september 2017, georganiseerd door het Hoogheemraadschap van Rijnland in het kader van de Groene Thema Cirkel Water, is met diverse partijen uit het gebied het beeld besproken en zijn een aantal verhaallijnen afgeleid. Deze verhaallijnen worden verder verwerkt in de ‘story maps’ van de klimaateffectatlas Zuid Holland.
    De kracht van sport in de wijk voor: Kwetsbare jongeren
    Goor, Roel van; Super, Sabina ; Holman, Marije - \ 2017
    In: Kracht van Sport in de Wijk / Vervoorn, Cees, Deutekom, Marije, Dekkers, Vera, - p. 29 - 46.
    Lezingenreeks 2017: Kracht van Sport in de Wijk

    Biedt sport kwetsbare jongeren meer structuur in hun dagelijkse leven? Voelt een vluchteling zich eerder welkom door sportdeelname? Leert sport mensen met psychiatrische problemen beter om te gaan met tegenslag? In de vijfdelige lezingreeks ‘Kracht van Sport’ stond in 2017 de problematiek en inzet van sport bij diverse doelgroepen in de wijk centraal.

    In de lezingenreeks Kracht van Sport in de Wijk gingen experts op zoek naar manieren waarop welzijnswerkers, zorgverleners en professionals sport gezamenlijk als middel kunnen inzetten om de leefkwaliteit van wijkbewoners te verhogen.
    De kracht van sport in de wijk voor: Mensen met een beperking
    Kampen, Thomas ; Leenaars, Karlijn ; Weidemann, Kim - \ 2017
    In: Kracht van Sport in de Wijk / Vervoorn, Cees, Deutekom, Marije, Dekkers, Vera, - p. 13 - 28.
    Lezingenreeks 2017: Kracht van Sport in de Wijk

    Biedt sport kwetsbare jongeren meer structuur in hun dagelijkse leven? Voelt een vluchteling zich eerder welkom door sportdeelname? Leert sport mensen met psychiatrische problemen beter om te gaan met tegenslag? In de vijfdelige lezingreeks ‘Kracht van Sport’ stond in 2017 de problematiek en inzet van sport bij diverse doelgroepen in de wijk centraal.

    In de lezingenreeks Kracht van Sport in de Wijk gingen experts op zoek naar manieren waarop welzijnswerkers, zorgverleners en professionals sport gezamenlijk als middel kunnen inzetten om de leefkwaliteit van wijkbewoners te verhogen.
    Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens
    Cheng, X. ; Etalo, Desalegn W. ; Mortel, J.E. van de; Dekkers, E. ; Nguyen, Linh ; Medema, M.H. ; Raaijmakers, J.M. - \ 2017
    Environmental Microbiology 19 (2017)11. - ISSN 1462-2912 - p. 4638 - 4656.
    Pseudomonas fluorescens strain SS101 (Pf.SS101) promotes growth of Arabidopsis thaliana, enhances greening and lateral root formation, and induces systemic resistance (ISR) against the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). Here, targeted and untargeted approaches were adopted to identify bacterial determinants and underlying mechanisms involved in plant growth promotion and ISR by Pf.SS101. Based on targeted analyses, no evidence was found for volatiles, lipopeptides and siderophores in plant growth promotion by Pf.SS101. Untargeted, genome-wide analyses of 7488 random transposon mutants of Pf.SS101 led to the identification of 21 mutants defective in both plant growth promotion and ISR. Many of these mutants, however, were auxotrophic and impaired in root colonization. Genetic analysis of three mutants followed by site-directed mutagenesis, genetic complementation and plant bioassays revealed the involvement of the phosphogluconate dehydratase gene edd, the response regulator gene colR and the adenylsulfate reductase gene cysH in both plant growth promotion and ISR. Subsequent comparative plant transcriptomics analyses strongly suggest that modulation of sulfur assimilation, auxin biosynthesis and transport, steroid biosynthesis and carbohydrate metabolism in Arabidopsis are key mechanisms linked to growth promotion and ISR by Pf.SS101.
    The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows
    Hardie, L.C. ; VandeHaar, M.J. ; Tempelman, R.J. ; Weigel, K.A. ; Armentano, L.E. ; Wiggans, G.R. ; Veerkamp, R.F. ; Haas, Y. de; Coffey, M.P. ; Connor, E.E. ; Hanigan, M.D. ; Staples, C.R. ; Wang, Z. ; Dekkers, J.C.M. ; Spurlock, D.M. - \ 2017
    Journal of Dairy Science 100 (2017)11. - ISSN 0022-0302 - p. 9061 - 9075.
    Dairy - Feed efficiency - Genome-wide association study - Residual feed intake

    The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain β-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output.

    Zinc absorption from milk is affected by dilution but not by thermal processing, and milk enhances absorption of Zinc from high-phytate rice in young dutch women
    Talsma, Elise F. ; Moretti, Diego ; Ly, Sou Chheng ; Dekkers, Renske ; Heuvel, Ellen G.H.M. van den; Fitri, Aditia ; Boelsma, Esther ; Stomph, Tjeerd Jan ; Zeder, Christophe ; Melse-Boonstra, Alida - \ 2017
    The Journal of Nutrition 147 (2017)6. - ISSN 0022-3166 - p. 1086 - 1093.
    Absorption - Food processing - Human - Isotope dilution - Milk - Phytate - Rice - Thermal processing - Zinc

    Background: Milk has been suggested to increase zinc absorption. The effect of processing and the ability of milk to enhance zinc absorption from other foods has not been measured directly in humans. Objective: We aimed to assess zinc absorption from 1) milk undergoing various processing and preparatory steps and 2) from intrinsically labeled high-phytate rice consumed with milk or water. Methods: Two randomized crossover studies were conducted in healthy young women [age:18-25 y; body mass index (in kg/m2): 20-25]: 1) a milk study (n = 19) comparing the consumption of 800 mL full-fat ultra-high temperature (UHT) milk [heat-treated milk (HTM)], full-fat UHT milk diluted 1:1 with water [heat-treated milk and water (MW)], water, or unprocessed (raw) milk (UM), each extrinsically labeled with 67Zn, and 2) a rice study (n = 18) comparing the consumption of 90 g intrinsically 67Zn-labeled rice with 600 mL of water [rice and water (RW)] or fullfat UHT milk [rice and milk (RM)]. The fractional absorption of zinc (FAZ) was measured with the double-isotope tracer ratio method. In vitro, we assessed zinc extraction from rice blended into water, UM, or HTM with or without phytate. Results: FAZ from HTM was 25.5% (95% CI: 21.6%, 29.4%) and was not different from UM (27.8%; 95% CI: 24.2%, 31.4%). FAZ from water was higher (72.3%; 95% CI: 68.7%, 75.9%), whereas FAZ fromMWwas lower (19.7%; 95% CI: 17.5%, 21.9%) than HTM and UM (both P < 0.01). FAZ from RM (20.7%; 95% CI: 18.8%, 22.7%) was significantly higher than from RW (12.8%; 95% CI: 10.8%, 14.6%; P < 0.01). In vitro, HTM and UM showed several orders of magnitude higher extraction of zinc from rice with HTM than from rice with water at various phytate concentrations. Conclusions: Milk enhanced human FAZ from high-phytate rice by 62% compared with water. Diluting milk with water decreases its absorption-enhancing proprieties, whereas UHT processing does not.

    Use of multi-trait and random regression models to identify genetic variation in tolerance to porcine reproductive and respiratory syndrome virus
    Lough, Graham ; Rashidi, Hamed ; Kyriazakis, Ilias ; Dekkers, Jack C.M. ; Hess, Andrew ; Hess, Melanie ; Deeb, Nader ; Kause, Antti ; Lunney, Joan K. ; Rowland, Raymond R.R. ; Mulder, Herman ; Doeschl-Wilson, Andrea - \ 2017
    Genetics, Selection, Evolution 49 (2017)1. - ISSN 0999-193X - p. 1 - 15.

    Background: A host can adopt two response strategies to infection: resistance (reduce pathogen load) and tolerance (minimize impact of infection on performance). Both strategies may be under genetic control and could thus be targeted for genetic improvement. Although there is evidence that supports a genetic basis for resistance to porcine reproductive and respiratory syndrome (PRRS), it is not known whether pigs also differ genetically in tolerance. We determined to what extent pigs that have been shown to vary genetically in resistance to PRRS also exhibit genetic variation in tolerance. Multi-trait linear mixed models and random regression sire models were fitted to PRRS Host Genetics Consortium data from 1320 weaned pigs (offspring of 54 sires) that were experimentally infected with a virulent strain of PRRS virus to obtain genetic parameter estimates for resistance and tolerance. Resistance was defined as the inverse of within-host viral load (VL) from 0 to 21 (VL21) or 0 to 42 (VL42) days post-infection and tolerance as the slope of the reaction-norm of average daily gain (ADG21, ADG42) on VL21 or VL42. Results: Multi-trait analysis of ADG associated with either low or high VL was not indicative of genetic variation in tolerance. Similarly, random regression models for ADG21 and ADG42 with a tolerance slope fitted for each sire did not result in a better fit to the data than a model without genetic variation in tolerance. However, the distribution of data around average VL suggested possible confounding between level and slope estimates of the regression lines. Augmenting the data with simulated growth rates of non-infected half-sibs (ADG0) helped resolve this statistical confounding and indicated that genetic variation in tolerance to PRRS may exist if genetic correlations between ADG0 and ADG21 or ADG42 are low to moderate. Conclusions: Evidence for genetic variation in tolerance of pigs to PRRS was weak when based on data from infected piglets only. However, simulations indicated that genetic variance in tolerance may exist and could be detected if comparable data on uninfected relatives were available. In conclusion, of the two defense strategies, genetics of tolerance is more difficult to elucidate than genetics of resistance.

    Semi-quantitative proteomics of mammalian cells upon short-term exposure to nonionizing electromagnetic fields
    Kuzniar, Arnold ; Laffeber, Charlie ; Eppink, Berina ; Bezstarosti, Karel ; Dekkers, Dick ; Woelders, Henri ; Zwamborn, A.P.M. ; Demmers, Jeroen ; Lebbink, Joyce H.G. ; Kanaar, Roland - \ 2017
    PLoS ONE 12 (2017)2. - ISSN 1932-6203

    The potential effects of non-ionizing electromagnetic fields (EMFs), such as those emitted by power-lines (in extremely low frequency range), mobile cellular systems and wireless networking devices (in radio frequency range) on human health have been intensively researched and debated. However, how exposure to these EMFs may lead to biological changes underlying possible health effects is still unclear. To reveal EMF-induced molecular changes, unbiased experiments (without a priori focusing on specific biological processes) with sensitive readouts are required. We present the first proteome-wide semi-quantitative mass spectrometry analysis of human fibroblasts, osteosarcomas and mouse embryonic stem cells exposed to three types of non-ionizing EMFs (ELF 50 Hz, UMTS 2.1 GHz and WiFi 5.8 GHz). We performed controlled in vitro EMF exposures of metabolically labeled mammalian cells followed by reliable statistical analyses of differential protein-and pathway-level regulations using an array of established bioinformatics methods. Our results indicate that less than 1% of the quantitated human or mouse proteome responds to the EMFs by small changes in protein abundance. Further network-based analysis of the differentially regulated proteins did not detect significantly perturbed cellular processes or pathways in human and mouse cells in response to ELF, UMTS or WiFi exposure. In conclusion, our extensive bioinformatics analyses of semi-quantitative mass spectrometry data do not support the notion that the short-time exposures to non-ionizing EMFs have a consistent biologically significant bearing on mammalian cells in culture.

    Stekende insecten rondom de Groote Peel : nulmeting 2016
    Verdonschot, Piet F.M. ; Dekkers, Dorine D. - \ 2017
    Wageningen : Wageningen Environmental Research (Alterra), Zoetwatersystemen (Notitie / Zoetwaterecosystemen, Wageningen Environmental Research ) - ISBN 9789463431231 - 40
    culicidae - steken (activiteit) - insecten - hoogveengebieden - moerassen - noord-brabant - culicidae - stinging - insects - moorlands - marshes - noord-brabant
    Het doel van het project ‘Stekende insecten rondom de Groote Peel’ is tweeledig: a) Het verrichten van een Quick-scan risico-analyse van het gebied Groote Peel en met name de mogelijke effecten van de voorgenomen maatregelen in het project LIFE+ op eventuele overlast veroorzaakt door steekmuggen en knutten. b) Het in 2016 rondom de Groote Peel uitvoeren van een nulmeting om inzicht te krijgen in en het vastleggen van het voorkomen van steekmuggen en knutten rondom de lokaal aanwezige bebouwing en nabij natte randzones.
    Stekende insecten Griendtsveen 2016
    Verdonschot, Piet F.M. ; Dekkers, Dorine D. - \ 2017
    Wageningen : Wageningen Environmental Research (Alterra), Zoetwatersystemen (Notitie / Zoetwaterecosystemen, Wageningen Environmental Research ) - ISBN 9789463431248 - 81
    insecten - steken (activiteit) - culicidae - moerassen - hoogveengebieden - noord-brabant - insects - stinging - culicidae - marshes - moorlands - noord-brabant
    Het doel van het project is het terugdringen van de steekmuggenoverlast in Griendtsveen door: 1) Het in het maatregelenpakket van LIFE+ in de Mariapeel opnemen van een aangepast peilbeheer om de ontwikkeling van langdurig tijdelijke wateren tegen te gaan en de isolatie van langdurig tijdelijke wateren op te heffen. Hiervoor dienen de langdurig tijdelijke wateren die functioneren als broedplaats voor moerassteekmuggen te worden gekarteerd en dient de gebiedshydrologie en –morfologie te worden vastgelegd om doelgerichte maatregelen te kunnen formuleren. 2) Het instellen van een monitoringsmeetnet om de overlast van stekende insecten in en rondom het dorp Griendtsveen te kunnen volgen in de tijd. 3) Eventueel de verbindingszone waarlangs moerassteekmuggen migreren van het natuurgebied naar het dorp zo in te richten dat deze dient als barrière voor stekende insecten.
    Monitoring effecten zandsuppletie Leuvenumse beek 2016
    Verdonschot, Ralf ; Dekkers, Dorine ; Verdonschot, Piet - \ 2017
    Wageningen : Wageningen Environmental Research - ISBN 9789463431170 - 34
    waterlopen - herstel - ecologisch herstel - zandsuppletie - macrofauna - gelderland - streams - rehabilitation - ecological restoration - sand suppletion - macrofauna - gelderland
    In de Leuvenumse beek wordt vanaf 2014 het suppleren van zand als beekherstelmaatregel toegepast door Waterschap Vallei en Veluwe en Natuurmonumenten. Omdat over deze relatief nieuwe maatregel nog niet veel kennis voorhanden is, worden sindsdien de hydromorfologische en biologische ontwikkelingen gevolgd. In 2016 zijn in een aantal suppletietrajecten metingen verricht aan het profiel van de beekbodem, zijn substraatschattingen en metingen aan stroomsnelheid en diepte van de beek verricht en is de samenstelling van de macrofaunalevensgemeenschap onderzocht met behulp van een quickscan-techniek. De macrofauna- en substraatmetingen zijn een herhaling van metingen in 2014, zodat de ontwikkeling in de tijd is vastgelegd.
    The Gediz River fluvial archive : A benchmark for Quaternary research in Western Anatolia
    Maddy, D. ; Veldkamp, A. ; Demir, T. ; Gorp, W. van; Wijbrans, J.R. ; Hinsbergen, D.J.J. van; Dekkers, M.J. ; Schreve, D. ; Schoorl, J.M. ; Scaife, R. - \ 2017
    Quaternary Science Reviews 166 (2017). - ISSN 0277-3791 - p. 289 - 306.
    Buried river terraces - Fluvial archive - Gediz River - Pleistocene
    The Gediz River, one of the principal rivers of Western Anatolia, has an extensive Pleistocene fluvial archive that potentially offers a unique window into fluvial system behaviour on the western margins of Asia during the Quaternary. In this paper we review our work on the Quaternary Gediz River Project (2001-2010) and present new data which leads to a revised stratigraphical model for the Early Pleistocene development of this fluvial system.In previous work we confirmed the preservation of eleven buried Early Pleistocene fluvial terraces of the Gediz River (designated GT11, the oldest and highest, to GT1, the youngest and lowest) which lie beneath the basalt-covered plateaux of the Kula Volcanic Province. Deciphering the information locked in this fluvial archive requires the construction of a robust geochronology. Fortunately, the Gediz archive provides ample opportunity for age-constraint based upon age estimates derived from basaltic lava flows that repeatedly entered the palaeo-Gediz valley floors. In this paper we present, for the first time, our complete dataset of 40Ar/39Ar age estimates and associated palaeomagnetic measurements. These data, which can be directly related to the underlying fluvial deposits, provide age constraints critical to our understanding of this sequence.The new chronology establishes the onset of Quaternary volcanism at ∼1320ka (MIS42). This volcanism, which is associated with GT6, confirms a pre-MIS42 age for terraces GT11-GT7. Evidence from the colluvial sequences directly overlying these early terraces suggests that they formed in response to hydrological and sediment budget changes forced by climate-driven vegetation change. The cyclic formation of terraces and their timing suggests they represent the obliquity-driven climate changes of the Early Pleistocene. By way of contrast the GT5-GT1 terrace sequence, constrained by a lava flow with an age estimate of ∼1247ka, span the time-interval MIS42 - MIS38 and therefore do not match the frequency of climate change as previously suggested. The onset of volcanism breaks the simple linkage of terracing to climate-driven change. These younger terraces more likely reflect a localized terracing process triggered by base level changes forced by volcanic eruptions and associated reactivation of pre-existing faults, lava dam construction, landsliding and subsequent lava-dammed lake drainage.Establishing a firm stratigraphy and geochronology for the Early Pleistocene archive provides a secure framework for future exploitation of this part of the archive and sets the standard as we begin our work on the Middle-Late Pleistocene sequence. We believe this work forms a benchmark study for detailed Quaternary research in Turkey.
    DELAY OF GERMINATION 1 plays a role in Arabidopsis seed maturation
    Dekkers, Bas ; He, Hanzi ; Hanson, Johannes ; Willems, Leo ; Cueff, Gwendal ; Rajjou, Loïc ; Hilhorst, Henk ; Bentsink, Leonie - \ 2016
    Wageningen University
    GSE65471 - Arabidopsis thaliana - GSE65471 - Arabidopsis thaliana - PRJNA274129
    We analysed the transcriptome of dry seeds (the end product of seed maturation) of three genotypes with different DOG1 expression levels. These included the WT Ler (low DOG1 expression), the near isogenic line NILDOG1-Cvi (strong DOG1 expression) and the non-dormant dog1-1 mutant (absence of DOG1 expression). NILDOG1-Cvi is the Ler WT containing an introgression of the Cvi accession on chromosome 5, which includes the DOG1 gene (Bentsink et al., 2006). The dog1-1 mutant is in the NILDOG1-Cvi genetic background.
    Dormant and after-ripened seeds are distinguished by early transcriptional differences in the imbibed state
    Dekkers, Bas ; Pearce, Simon P. ; Bolderen-Veldkamp, Marieke van; Holdsworth, Michael J. ; Bentsink, Leonie - \ 2016
    Wageningen University
    Arabidopsis thaliana - GSE76907 - Arabidopsis thaliana - GSE76907 - PRJNA308922
    We analyzed the transcriptome of dormant and after-ripened imbibed seeds of the Arabidopsis accession Cape verde Islands.
    Can we select for both resistance and tolerance of pigs to PRRS?
    Lough, G. ; Rashidi, H. ; Kyriazakis, Ilias ; Deeb, N. ; Dekkers, J.C.M. ; Lunney, J.K. ; Rowland, R. ; Mulder, H.A. ; Doeschl-Wilson, A. - \ 2016
    In: Book of Abstracts of the 67st Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (Book of abstracts 22) - ISBN 9789086862849 - p. 318 - 318.
    Dormant and after-ripened Arabidopsis thaliana seeds are distinguished by early transcriptional differences in the imbibed state
    Dekkers, Bas J.W. ; Pearce, Simon P. ; Bolderen-Veldkamp, Marieke van; Holdsworth, Michael J. ; Bentsink, Leónie - \ 2016
    Frontiers in Plant Science 7 (2016). - ISSN 1664-462X
    After-ripening - Arabidopsis - Dormancy - Embryo - Endosperm - Seed - Transcriptome

    Seed dormancy is a genetically controlled block preventing the germination of imbibed seeds in favorable conditions. It requires a period of dry storage (after-ripening) or certain environmental conditions to be overcome. Dormancy is an important seed trait, which is under selective pressure, to control the seasonal timing of seed germination. Dormant and non-dormant (after-ripened) seeds are characterized by large sets of differentially expressed genes. However, little information is available concerning the temporal and spatial transcriptional changes during early stages of rehydration in dormant and nondormant seeds. We employed genome-wide transcriptome analysis on seeds of the model plant Arabidopsis thaliana to investigate transcriptional changes in dry seeds upon rehydration. We analyzed gene expression of dormant and after-ripened seeds of the Cvi accession over four time points and two seed compartments (the embryo and surrounding single cell layer endosperm), during the first 24 h after sowing. This work provides a global view of gene expression changes in dormant and non-dormant seeds with temporal and spatial detail, and these may be visualized via a web accessible tool (http://www.wageningenseedlab.nl/resources). A large proportion of transcripts change similarly in both dormant and non-dormant seeds upon rehydration, however, the first differences in transcript abundances become visible shortly after the initiation of imbibition, indicating that changes induced by after-ripening are detected and responded to rapidly upon rehydration. We identified several gene expression profiles which contribute to differential gene expression between dormant and non-dormant samples. Genes with enhanced expression in the endosperm of dormant seeds were overrepresented for stress-related Gene Ontology categories, suggesting a protective role for the endosperm against biotic and abiotic stress to support persistence of the dormant seed in its environment.

    The price of Dutch (Urban) Design: Measuring the impact of neighbourhood layout on house values - Presenting the research framework’
    Dekkers, J. ; Groot, J. de; Brink, A. van den - \ 2016
    Food Structure and Functionality Forum
    Dekkers, Birgit - \ 2016
    Presentation with subject: Towards understanding of the formation of layered and fibrous structures in dense biopolymer blends
    Food Colloids 2016
    Dekkers, Birgit - \ 2016
    Presentation with subject: Fibrous structures from a condensed water-in-water emulsion by simple shear flow deformation
    Impact of fitting dominance and additive effects on accuracy of genomic prediction of breeding values in layers
    Heidaritabar, M. ; Wolc, A. ; Arango, J. ; Zeng, J. ; Settar, P. ; Fulton, J.E. ; O'Sullivan, N.P. ; Bastiaansen, J.W.M. ; Fernando, R.L. ; Garrick, D.J. ; Dekkers, J.C.M. - \ 2016
    Journal of Animal Breeding and Genetics 133 (2016). - ISSN 0931-2668 - p. 334 - 346.
    Additive effect - Dominance effect - Genomic selection - Layer

    Most genomic prediction studies fit only additive effects in models to estimate genomic breeding values (GEBV). However, if dominance genetic effects are an important source of variation for complex traits, accounting for them may improve the accuracy of GEBV. We investigated the effect of fitting dominance and additive effects on the accuracy of GEBV for eight egg production and quality traits in a purebred line of brown layers using pedigree or genomic information (42K single-nucleotide polymorphism (SNP) panel). Phenotypes were corrected for the effect of hatch date. Additive and dominance genetic variances were estimated using genomic-based [genomic best linear unbiased prediction (GBLUP)-REML and BayesC] and pedigree-based (PBLUP-REML) methods. Breeding values were predicted using a model that included both additive and dominance effects and a model that included only additive effects. The reference population consisted of approximately 1800 animals hatched between 2004 and 2009, while approximately 300 young animals hatched in 2010 were used for validation. Accuracy of prediction was computed as the correlation between phenotypes and estimated breeding values of the validation animals divided by the square root of the estimate of heritability in the whole population. The proportion of dominance variance to total phenotypic variance ranged from 0.03 to 0.22 with PBLUP-REML across traits, from 0 to 0.03 with GBLUP-REML and from 0.01 to 0.05 with BayesC. Accuracies of GEBV ranged from 0.28 to 0.60 across traits. Inclusion of dominance effects did not improve the accuracy of GEBV, and differences in their accuracies between genomic-based methods were small (0.01-0.05), with GBLUP-REML yielding higher prediction accuracies than BayesC for egg production, egg colour and yolk weight, while BayesC yielded higher accuracies than GBLUP-REML for the other traits. In conclusion, fitting dominance effects did not impact accuracy of genomic prediction of breeding values in this population.

    Shear-induced fibrous structure formation from a pectin/SPI blend
    Dekkers, Birgit L. ; Nikiforidis, Costas ; Goot, Atze Jan van der - \ 2016
    Innovative Food Science and Emerging Technologies 36 (2016). - ISSN 1466-8564 - p. 193 - 200.
    Biopolymer incompatibility - Fibrous structure - High temperature shear cell - Protein-polysaccharide blend - Shear-induced structuring

    Well-defined shear flow can be applied to create fibrous, anisotropic samples from biopolymers when present at sufficiently high dry matter contents. Anisotropic biopolymer structures are of high interest especially when made from plant-based polymer blends due to novel food applications, like meat replacers. We investigate shear-induced structuring of a pectin/soy protein isolate (SPI) blend under heating. Scanning Electron Microscope analysis revealed that shear-induced structuring resulted in elongated pectin filaments, oriented in the direction of the shear flow, being entrapped in a continuous protein phase, inducing anisotropy in the blend. The length of the pectin filaments increased upon higher pectin concentrations and shearing temperatures, leading both to higher anisotropy, as measured with the tensile strength analysis. The fibrous appearance of samples became more evident when deforming the product by tearing, which effect was thought to be caused by detachment through or along the long side of the pectin filament. Industrial relevance The efficient preparation of fibrous products based on plant materials is of interest, because these products can be a starting point for the development of meat replacers. Meat replacers made from plant material are a promising, innovative, and sustainable source of protein for human consumption. With an increasing world population, creation of innovative sources of protein are needed to be able to feed everyone (United Nations - Department of Economic and Social Affairs, 2015). Proteins from plant sources, such as soy, are preferred over proteins from animal origin because plant based materials, for example, have lower environmental impact (Day, 2013; Mogensen, Hermansen, Halberg, Dalgaard, R., Vis, & Smith, 2009). In order to replace meat by a plant-based meat replacer, it is important that a similar product in terms of structural properties is developed to improve consumer acceptance (Hoek et al., 2011). Meat replacers are often produced with extrusion cooking, which is a process that has been applied for texturization of plant materials in the application of meat replacers for decades (Campbell, 1981; Harper & Clark, 1978). Previous research showed that a novel technique based on well-defined shear flow can also be used to create fibrous, anisotropic structures from plant-based biopolymers at sufficiently high dry matter contents, with a cone–cone device (Shear Cell) or a concentric cylinder device (Couette Cell) (Grabowska, Tekidou, Boom, & van der Goot, 2014; G. A. Krintiras, Göbel, Bouwman, van der Goot, & Stefanidis, 2014; Manski, van der Goot, & Boom, 2007). This novel technique uses milder conditions for structure formation, due to lower applied shear forces, and has therefore a lower specific mechanical energy input (Grabowska et al., 2016; G.A. Krintiras, Gadea Diaz, van der Goot, Stankiewicz, & Stefanidis, 2015).

    Shear-induced structuring as a tool to make anisotropic materials using soy protein concentrate
    Grabowska, Katarzyna J. ; Zhu, Sicong ; Dekkers, Birgit L. ; Ruijter, Norbert C.A. de; Gieteling, Jarno ; Goot, Atze J. van der - \ 2016
    Journal of Food Engineering 188 (2016). - ISSN 0260-8774 - p. 77 - 86.
    Fibrous structure - Shear - Shearing equipment - Soy protein concentrate

    This research presents the formation of anisotropic, and partly fibrous, semi-solid structures with Soy Protein Concentrate (SPC) using the concept of shear-induced structuring. The morphological and mechanical properties of the structures obtained are analyzed using confocal scanning laser microscopy (CSLM), and large scale mechanical deformation analysis. We present process conditions leading to the formation of anisotropic structures in SPC and found that comparable conditions did not result in anisotropy when using soy protein isolate. Results indicate the importance of the dry matter content, the process temperature and the presence of carbohydrates in structure formation. CSLM pictures show that carbohydrates form a separate phase in the system, which is oriented upon processing. The need for high temperatures also required the development of next generation shearing equipment.

    Post-embryonic Hourglass Patterns Mark Ontogenetic Transitions in Plant Development
    Drost, Hajk Georg ; Bellstädt, Julia ; Ó'Maoiléidigh, Diarmuid S. ; Silva, Anderson T. ; Gabel, Alexander ; Weinholdt, Claus ; Ryan, Patrick T. ; Dekkers, Bas J.W. ; Bentsink, Leónie ; Hilhorst, Henk W.M. ; Ligterink, Wilco ; Wellmer, Frank ; Grosse, Ivo ; Quint, Marcel - \ 2016
    Molecular Biology and Evolution 33 (2016)5. - ISSN 0737-4038 - p. 1158 - 1163.
    developmental hourglass - floral transition - germination - plant development - transcriptomics

    The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found postembryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.

    A combined rheology and time domain NMR approach for determining water distributions in protein blends
    Dekkers, Birgit L. ; Kort, Daan W. de; Grabowska, Katarzyna J. ; Tian, Bei ; As, Henk Van; Goot, Atze Jan van der - \ 2016
    Food Hydrocolloids 60 (2016). - ISSN 0268-005X - p. 525 - 532.
    Concentrated blend - Plant protein - Polymer blending law - Rheology - Time domain NMR

    We present a combined time domain NMR and rheology approach to quantify the water distribution in a phase separated protein blend. The approach forms the basis for a new tool to assess the microstructural properties of phase separated biopolymer blends, making it highly relevant for many food and non-food related applications. First, we determine the relaxation rate of absorbed water, and the viscoelastic properties of the separated phases as function of the water content. Next, the same properties are measured for the protein blends. Finally, predictions for water distribution obtained from rheological experiments are made via the polymer blending law, and compared to a more direct assessment of the water distribution with time-domain NMR relaxometry (TD-NMR). In this study, the protein blend consists of soy protein isolate (SPI) and vital wheat gluten (WG). We demonstrate that predictions for water distribution are similar for both TD-NMR and rheological measurements. It turns out that water does not distribute homogenously over the phases. Independent of the SPI and WG ratio, more water is absorbed by the SPI phase relative to the WG phase, which largely determines the resulting rheological properties of the blends.

    Zandsuppletie in de Leuvenumse beek: monitoring van de fysische en biologische effecten 2014-2015
    Verdonschot, R.C.M. ; Dekkers, T.B.M. ; Besse-Lototskaya, A.A. ; Verdonschot, P.F.M. - \ 2016
    Wageningen : Alterra, Wageningen-UR - ISBN 9789462577886 - 51
    zandsuppletie - zand - waterlopen - macrofauna - gelderland - sand suppletion - sand - streams - macrofauna - gelderland
    In 2014-2105 zijn de fysische en biologische korte-termijn-effecten van het herhaaldelijk suppleren van zand op een drietal locaties in de Leuvenumse beek onderzocht. Er is gekeken naar de mate van ophoging en verspoeling van het ingebrachte zand, de interactie tussen het zand en houtpakketten, de consequenties van depositie van organisch materiaal als gevolg van verstuwing van de beek en tenslotte naar de effecten op de macrofauna.
    Galactinol as marker for seed longevity
    Souza Vidigal, D. De; Willems, L.A.J. ; Arkel, J. van; Dekkers, S.J.W. ; Hilhorst, H.W.M. ; Bentsink, L. - \ 2016
    Plant Science 246 (2016). - ISSN 0168-9452 - p. 112 - 118.
    Reduced seed longevity or storability is a major problem in seed storage and contributes to increasedcosts in crop production. Here we investigated whether seed galactinol contents could be predictive forseed storability behavior in Arabidopsis, cabbage and tomato. The analyses revealed a positive correla-tion between galactinol content and seed longevity in the three species tested, which indicates that thiscorrelation is conserved in the Brassicaceae and beyond. Quantitative trait loci (QTL) mapping in tomatorevealed a co-locating QTL for galactinol content and seed longevity on chromosome 2. A candidate for thisQTL is the GALACTINOL SYNTHASE gene (Solyc02g084980.2.1) that is located in the QTL interval. GALACTI-NOL SYNTHASE is a key enzyme of the raffinose family oligosaccharide (RFO) pathway. To investigate therole of enzymes in the RFO pathway in more detail, we applied a reverse genetics approach using T-DNAknock-out lines in genes encoding enzymes of this pathway (GALACTINOL SYNTHASE 1, GALACTINOL SYN-THASE 2, RAFFINOSE SYNTHASE, STACHYOSE SYNTHASE and ALPHA-GALACTOSIDASE) and overexpressorsof the cucumber GALACTINOL SYNTHASE 2 gene in Arabidopsis. The galactinol synthase 2 mutant and thegalactinol synthase 1 galactinol synthase 2 double mutant contained the lowest seed galactinol contentwhich coincided with lower seed longevity. These results show that galactinol content of mature dryseed can be used as a biomarker for seed longevity in Brassicaceae and tomato.
    Impact of gastric pH profiles on the proteolytic digestion of mixed βlg-Xanthan biopolymer gels
    Dekkers, B.L. ; Kolodziejczyk, E. ; Acquistapace, S. ; Engmann, J. ; Wooster, T.J. - \ 2016
    Food & Function 7 (2016)1. - ISSN 2042-6496 - p. 58 - 68.

    The understanding of how foods are digested and metabolised is essential to enable the design/selection of foods as part of a balanced diet. Essential to this endeavour is the development of appropriate biorelevant in vitro digestion tools. In this work, the influence of gastric pH profile on the in vitro digestion of mixtures of β-lactoglobulin (βlg) and xanthan gum prior to and after heat induced gelation was investigated. A conventional highly acidic (pH 1.9) gastric pH profile was compared to two dynamic gastric pH profiles (initial pH of 6.0 vs. 5.2 and H+ secretion rates of 60 vs. 36 mmol h-1) designed to mimic the changes in gastric pH observed during clinical trials with high protein meals. In moving away from the pH 1.9 model, to a pH profile reflecting in vivo conditions, the initial rate and degree of protein digestion halved during the first 45 minutes. After 90 minutes of gastric digestion, all three pH profiles caused similar extents of protein digestion. Given that 50% gastric emptying times of (test) meals are in range of 30-90 min, it would seem highly relevant to use a dynamic pH gastric model rather than a pH 1.9 (USP) or pH 3 model (INFOGEST) in assessing the impact of food structuring approaches on protein digestion. The impact that heat induced gelation had on the degree of gel digestion by pepsin was also investigated. Surprisingly, it was found that heat induced gelation of βlg-xanthan mixtures at 70-90°C for 20 minutes lead to a considerable decrease in the rate of proteolysis, which contrasts many studies of dispersed aggregates and gels of βlg alone whose heating accelerates pepsin activity due to unfolding. In the present case, the formation of a dense protein network created a fine pore structure which restricted pepsin access into the gel thereby slowing proteolysis. This work not only has implications for the in vitro assessment of protein digestion, but also highlights how protein digestion might be slowed, learnings that might have an influence on the design of foods as part of a satisfying balanced diet.

    The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development
    Dekkers, B.J.W. ; He, Hanzi ; Hanson, Johannes ; Willems, L.A.J. ; Jamar, D.C.L. ; Cueff, Gwendal ; Rajjou, Loïc ; Hilhorst, H.W.M. ; Bentsink, Leónie - \ 2016
    The Plant Journal 85 (2016)4. - ISSN 0960-7412 - p. 451 - 465.
    ABA insensitive - Abscisic acid - Arabidopsis thaliana (Arabidopsis) - DELAY OF GERMINATION - Dormancy - Seed development - Seed maturation

    The seed expressed gene DELAY OF GERMINATION (DOG) 1 is absolutely required for the induction of dormancy. Next to a non-dormant phenotype, the dog1-1 mutant is also characterized by a reduced seed longevity suggesting that DOG1 may affect additional seed processes as well. This aspect however, has been hardly studied and is poorly understood. To uncover additional roles of DOG1 in seeds we performed a detailed analysis of the dog1 mutant using both transcriptomics and metabolomics to investigate the molecular consequences of a dysfunctional DOG1 gene. Further, we used a genetic approach taking advantage of the weak aba insensitive (abi) 3-1 allele as a sensitized genetic background in a cross with dog1-1. DOG1 affects the expression of hundreds of genes including LATE EMBRYOGENESIS ABUNDANT and HEAT SHOCK PROTEIN genes which are affected by DOG1 partly via control of ABI5 expression. Furthermore, the content of a subset of primary metabolites, which normally accumulate during seed maturation, was found to be affected in the dog1-1 mutant. Surprisingly, the abi3-1 dog1-1 double mutant produced green seeds which are highly ABA insensitive, phenocopying severe abi3 mutants, indicating that dog1-1 acts as an enhancer of the weak abi3-1 allele and thus revealing a genetic interaction between both genes. Analysis of the dog1 and dog1 abi3 mutants revealed additional seed phenotypes and therefore we hypothesize that DOG1 function is not limited to dormancy but that it is required for multiple aspects of seed maturation, in part by interfering with ABA signalling components.

    The Blake Event recorded near the Eemian type locality – A diachronic onset of the Eemian in Europe
    Sier, Mark J. ; Peeters, Jan ; Dekkers, Mark J. ; Pares, Josep M. ; Chang, L. ; Busschers, F.S. ; Cohen, Kim M. ; Wallinga, J. ; Bunnik, F.P.M. ; Roebroeks, W. - \ 2015
    Quaternary Geochronology 28 (2015). - ISSN 1871-1014 - p. 12 - 28.
    Land-sea correlation; Last interglacial; MIS 5e; North Sea Basin
    Multidisciplinary analysis including paleomagnetic, sedimentologic, sea-level change, luminescence dating and palynologic research was performed on a 25 m long orientated core taken at Rutten, close to Eemian key localities in the Netherlands. The main goal of our research was to test a possible delayed onset of temperate conditions in this region compared to Southern Europe, occurring within the Last Interglacial. The sediments revealed the presence of the paleomagnetic Blake Event in ca. 10 m of lower-deltaic floodbasin sediments that contain a pollen record covering the Eemian. The position of the Blake Event in relation to the pollen stratigraphy concurs with the earlier studied Neumark Nord 2 site. Paleomagnetic correlation to core MD95-2042 off SW Iberia indicates ca. 5 kyr diachroneity between the pollen-based onset of temperate interglacial conditions between northern and southern Europe. The onset of the Eemian in north-western and central Europe (ca. 121.0 ka) post-dates the Marine Isotope Stage 6/5e transition by ca. 10 kyr. In addition, the Rutten data provide evidence for a relatively long duration of the Blake Event of at least 8 kyr. The late onset of the temperate conditions that define the base of the Eemian, imply that NW Europe with the Eemian type area is not the most suited region to define the beginning of the Last Interglacial and Late Pleistocene for global chronostratigraphic use.

    Stekende insecten Griendtsveen : situatie 2015
    Verdonschot, P.F.M. ; Dekkers, T.B.M. ; Besse-Lototskaya, A.A. - \ 2015
    Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2680)
    culicidae - insecten - steken - steken (activiteit) - limburg - waterstand - culicidae - insects - stings - stinging - limburg - water level
    Naar aanleiding van het advies van de Tijdelijke Adviescommissie LIFE+ Mariapeel om een onderzoek naar de muggenoverlast te verrichten is door de gemeente Horst aan de Maas gezamenlijk met de provincie Limburg een onderzoeksopdracht aan Alterra – Wageningen UR verstrekt. Alterra is gevraagd om de muggenoverlast te monitoren en daarmee de nulsituatie vast te stellen, de mate van overlast aan te geven en te adviseren over de effecten van voorgenomen maatregelen op de overlast.
    Onderzoek naar Brucella bij wilde zwijnen op de Veluwe
    Tulden, P.W. van; Dekkers, L.J.M. ; Giessen, J. van der - \ 2015
    Jacht & Beheer (2015). - ISSN 1569-3414 - p. 14 - 14.
    Regulation of seed dormancy by abscisic acid and DELAY OF Germination 1
    Dekkers, S.J.W. ; Bentsink, L. - \ 2015
    Seed Science Research 25 (2015)02. - ISSN 0960-2585 - p. 82 - 98.
    Physiological dormancy has been described as a physiological inhibiting mechanism that prevents radicle emergence. It can be caused by the embryo (embryo dormancy) as well as by the structures that cover the embryo. One of its functions is to time plant growth and reproduction to the most optimal season and therefore, in nature, dormancy is an important adaptive trait that is under selective pressure. Dormancy is a complex trait that is affected by many loci, as well as by an intricate web of plant hormone interactions. Moreover, it is strongly affected by a multitude of environmental factors. Its induction, maintenance, cycling and loss come down to the central paradigm, which is the balance between two key hormonal regulators, i.e. the plant hormone abscisic acid (ABA), which is required for dormancy induction, and gibberellins (GA), which are required for germination. In this review we will summarize recent developments in dormancy research (mainly) in the model plant Arabidopsis thaliana, focusing on two key players for dormancy induction, i.e. the plant hormone ABA and the DELAY OF GERMINATION 1 (DOG1) gene. We will address the role of ABA and DOG1 in relation to various aspects of seed dormancy, i.e. induction during seed maturation, loss during dry seed afterripening, the rehydrated state (including dormancy cycling) and the switch to germination.
    Acquisition and loss of desiccation tolerance in seeds:from experimental model to biological relevance
    Dekkers, S.J.W. ; Dias Costa, M.C. ; Maia, J. ; Bentsink, L. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2015
    Planta 241 (2015)3. - ISSN 0032-0935 - p. 563 - 577.
    Main conclusion Besides being an important model to study desiccation tolerance, the induction of desiccation tolerance in germinated seeds may also play an ecological role in seedling establishment. Desiccation tolerance (DT) is the ability of certain organisms to survive extreme water losses without accumulation of lethal damage. This was a key feature in the conquering of dry land and is currently found in all taxa including bacteria, fungi, roundworms and plants. Not surprisingly, studies in various fields have been performed to unravel this intriguing phenomenon. In flowering plants, DT is rare in whole plants (vegetative tissues), yet is common in seeds. In this review, we present our current understanding of the evolution of DT in plants. We focus on the acquisition of DT in seeds and the subsequent loss during and after germination by highlighting and comparing research in two model plants Medicago truncatula and Arabidopsis thaliana. Finally, we discuss the ability of seeds to re-establish DT during post-germination, the possible ecological meaning of this phenomenon, and the hypothesis that DT, in combination with dormancy, optimizes seedling establishment.
    Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds
    Voort, M. van der; Meijer, H.J.G. ; Schmidt, Y. ; Watrous, J. ; Dekkers, E. ; Mendes, R. ; Dorrestein, P.C. ; Gross, H. ; Raaijmakers, J.M. - \ 2015
    Frontiers in Microbiology 6 (2015). - ISSN 1664-302X - 14 p.
    ii secretion system - phytophthora-infestans - biological-activity - functional-analysis - mass-spectrometry - natural functions - phospholipase-d - corrugata - biocontrol - lipopeptides
    The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.
    Synergistic effects of drought and deforestation on the resilience of the south-eastern Amazon rainforest
    Staal, A. ; Dekkers, S. ; Hirota Magalhaes, M. ; Nes, E.H. van - \ 2015
    Ecological Complexity 22 (2015). - ISSN 1476-945X - p. 65 - 75.
    tropical tree cover - critical transitions - global resilience - african savannas - tipping points - linking theory - climate-change - woody cover - fire - feedbacks
    The south-eastern Amazon rainforest is subject to ongoing deforestation and is expected to become drier due to climate change. Recent analyses of the distribution of tree cover in the tropics show three modes that have been interpreted as representing alternative stable states: forest, savanna and treeless states. This situation implies that a change in environmental conditions, such as in the climate, could cause critical transitions from a forest towards a savanna ecosystem. Shifts to savanna might also occur if perturbations such as deforestation exceed a critical threshold. Recovering the forest would be difficult as the savanna will be stabilized by a feedback between tree cover and fire. Here we explore how environmental changes and perturbations affect the forest by using a simple model with alternative tree-cover states. We focus on the synergistic effects of precipitation reduction and deforestation on the probability of regime shifts in the south-eastern Amazon rainforest. The analysis indicated that in a large part of the south-eastern Amazon basin rainforest and savanna could be two alternative states, although massive forest dieback caused by mean-precipitation reduction alone is unlikely. However, combinations of deforestation and climate change triggered up to 6.6 times as many local regime shifts than the two did separately, causing large permanent forest losses in the studied region. The results emphasize the importance of reducing deforestation rates in order to prevent a climate-induced dieback of the south-eastern Amazon rainforest.
    The earliest securely-dated hominin artefact in Anatolia?
    Maddy, D. ; Schreve, D. ; Demir, T. ; Veldkamp, A. ; Wijbrans, J.R. ; Gorp, W. van; Hinsbergen, D.J.J. van; Dekkers, M.J. ; Scaife, R. ; Schoorl, J.M. ; Stemerdink, C. ; Schriek, T. van der - \ 2015
    Quaternary Science Reviews 109 (2015). - ISSN 0277-3791 - p. 68 - 75.
    geomagnetic secular variation - river terrace staircase - western turkey - gediz river - volcanic field - dmanisi - georgia - kula - dispersal - caucasus
    Anatolia lies at the gateway from Asia into Europe and has frequently been favoured as a route for Early Pleistocene hominin dispersal. Although early hominins are known to have occupied Turkey, with numerous finds of Lower Palaeolithic artefacts documented, the chronology of their dispersal has little reliable stratigraphical or geochronological constraint, sites are rare, and the region's hominin history remains poorly understood as a result. Here, we present a Palaeolithic artefact, a hard-hammer flake, from fluvial sediments associated with the Early Pleistocene Gediz River of Western Turkey. This previously documented buried river terrace sequence provides a clear stratigraphical context for the find and affords opportunities for independent age estimation using the numerous basaltic lava flows that emanated from nearby volcanic necks and aperiodically encroached onto the contemporary valley floors. New 40Ar/39Ar age estimates from these flows are reported here which, together with palaeomagnetic measurements, allow a tightly-constrained chronology for the artefact-bearing sediments to be established. These results suggest that hominin occupation of the valley occurred within a time period spanning ~1.24 Ma to ~1.17 Ma, making this the earliest, securely-dated, record of hominin occupation in Anatolia.
    Novel insights into the risk assessment of the nanomaterial synthetic amorphous silica, additive E551, in food
    Kesteren, P.C.E. van; Cubadda, F. ; Bouwmeester, H. ; Eijkeren, J.C.H. ; Dekkers, S. ; Jong, W.H. de; Oomen, A.G. - \ 2015
    Nanotoxicology 9 (2015)4. - ISSN 1743-5390 - p. 442 - 452.
    This study presents novel insights in the risk assessment of synthetic amorphous silica (SAS) in food. SAS is a nanostructured material consisting of aggregates and agglomerates of primary particles in the nanorange (
    Diptera larven (niet-Chironomidae)
    Dekkers, Dorine - \ 2014
    Juffer juwelen: Sieraden gemaakt door kokerjuffers
    Dekkers, T.B.M. ; Oosten-Siedlecka, A.M. van - \ 2014
    Landschap : tijdschrift voor landschapsecologie en milieukunde 3 (2014). - ISSN 0169-6300 - p. 169 - 171.
    aquatische ecologie - trichoptera - ontwikkelingsstadia - kunst - natuur- en milieueducatie - innovaties - aquatic ecology - trichoptera - developmental stages - arts - nature and environmental education - innovations
    Insecten en andere ongewervelden (in aquatische ecosystemen) bouwen vaak indrukwekkende constructies. De natuurlijke herkomst van die materialen zorgt voor camouflage die bescherming biedt tegen predatie. In Frankrijk zijn kokerjuffers gebruikt door een kunstenaar, voor het maken van sieraden. Maar ook wetenschappers van Alterra laten zich door hun kennis leiden.. Met als doel: het onder de aandacht brengen van waterinsecten bij volwassenen. Via aan de natuur ontleende "bouwwerken".
    Directional movement in response to altered flow in six lowland stream Trichoptera
    Verdonschot, P.F.M. ; Besse, A.A. ; Dekkers, T.B.M. ; Verdonschot, R.C.M. - \ 2014
    Hydrobiologia 740 (2014)1. - ISSN 0018-8158 - p. 219 - 230.
    lotic macroinvertebrates - benthic invertebrates - field experiments - upstream movements - river systems - drift - colonization - habitat - refugia - insect
    Understanding the trait adaptations associated with mobility in Trichoptera larvae under different flow conditions would enhance the understanding of survival mechanisms under flow stress induced by spates. In stream mesocosms, we mimicked a lowland stream spate by suddenly increasing current velocity above an organic habitat patch from 10 to 30 or 50 cm/s. Subsequently, we investigated whether short-term, small-scale movements in six Trichoptera species were not random but directional and whether the type of movement was related to the magnitude of flow increase. Main types of response distinguished were as follows: (1) resistance, in which the species remained in the habitat patch, (2) upstream or downstream crawling, and (3) being dislodged from the streambed and drift downstream (vulnerability). The type of response observed was related to the species’ ecological preferences and morphological traits. The experiment showed that movement in Trichoptera larvae was directional and flow-dependent. Drift was the main mechanism observed with an increase in current velocity, but upstream crawling and aggregation in the habitat patch were observed as well. The type and magnitude of the response were highly species specific. It appeared that each combination of morphological and behavioral adaptations developed individually for each species under niche-specific conditions.
    The contribution of plant uptake to nutrient removal by floating treatment wetlands
    Keizer-Vlek, H.E. ; Verdonschot, P.F.M. ; Verdonschot, R.C.M. ; Dekkers, T.B.M. - \ 2014
    Ecological Engineering 73 (2014). - ISSN 0925-8574 - p. 684 - 690.
    aquaculture waste-water - constructed wetlands - phosphorus - vegetation - runoff - system
    Floating treatment wetlands (FTWs) may provide an appealing alternative to the more conventional (sub) surface flow wetlands to solve problems associated with eutrophication in urban surface waters, because they do not claim additional land area. This study examined the contribution of plant uptake to overall removal capacity of FTWs. A batch mesocosm experiment was performed during the growing season using thirty 84 L polyethylene tanks covered with 0.28 m2 floating Styrofoam mats. Ten tanks served as a control (only Styrofoam cover), 10 tanks were planted with Iris pseudacorus, and 10 with Typha angustifolia. Nutrients were added weekly to keep total nitrogen (TN) and total phosphorous (TP) concentrations at approximately 4 mg N L-1 and 0.25 mg P L-1. Total removal of TN an TP from the treatment with Typha was relatively low, resulting from the limited increase in plant biomass during the experiment. Total removal of TN and TP from the tanks planted with Iris was 277 mg N m-2 d-1 and 9.32 mg P m-2 d-1 during the experiment. These values were significantly higher than the values for total removal from the control tanks, i.e., 54 times higher for TN removal and 10 times higher for TP removal. Plant uptake played a major role in the removal of nitrogen and phosphorous from the water by FTWs, i.e., 74% of TN removal and 60% of TP removal resulted from Iris uptake. These results suggest that FTWs planted with Iris can be applied in a temperate climate to overcome problems with excessive algae growth in surface waters.
    Identification of reference genes for gene expression studies during seed germination and seedling establishment Ricinus communis L.
    Ribeiro de Jesus, P.R. ; Dekkers, S.J.W. ; Fernandez, L.G. ; Castro, R.D. De; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
    Seed Science Research 24 (2014)4. - ISSN 0960-2585 - p. 341 - 352.
    time rt-pcr - fatty-acid - jatropha-curcas - castor-oil - phosphoenolpyruvate carboxylase - arabidopsis - normalization - plant - cloning - family
    Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an important technology to analyse gene expression levels during plant development or in response to different treatments. An important requirement to measure gene expression levels accurately is a properly validated set of reference genes. In this context, we analysed the potential use of 17 candidate reference genes across a diverse set of samples, including several tissues, different stages and environmental conditions, encompassing seed germination and seedling growth in Ricinus communis L. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. GeNorm and Normfinder indicated that ACT, POB and PP2AA1 comprise the optimal combination for normalization of gene expression data in inter-tissue (heterogeneous sample panel) studies. We also describe the optimal combination of reference genes for a subset of root, endosperm and cotyledon samples. In general, the most stable genes suggested by GeNorm are very consistent with those indicated by NormFinder, which highlights the strength of the selection of reference genes in our study. We also validated the selected reference genes by normalizing the expression levels of three target genes involved in energy metabolism with the reference genes suggested by GeNorm and NormFinder. The approach used in this study to identify stably expressed genes, and thus potential reference genes, was applied successfully for R. communis and it provides important guidelines for RT-qPCR studies in seeds and seedlings for other species (especially in those cases where extensive microarray data are not available)
    Predictive modelling of vegetable firmness after thermal pre-treatments and steaming
    Dekker, M. ; Dekkers, E. ; Jasper, A. ; Baár, C. ; Verkerk, R. - \ 2014
    Innovative Food Science and Emerging Technologies 25 (2014). - ISSN 1466-8564 - p. 14 - 18.
    pectin - kinetics - texture - fruits
    Texture is an important product property that strongly affects the quality evaluation of processed vegetables by consumers. The rate of texture decrease is dependent on the processing temperature and the type of vegetable. A large data set on instrumental texture measurements of carrot and broccoli was produced with different time–temperature combinations for steaming the vegetables. This data set was fitted with a fractional conversion model to describe the kinetics of texture change. Pre-treating the vegetables by steaming at 50–80 °C can increase the resistance towards softening in a subsequent steaming process. The effect of time and temperature of the thermal pre-treatment on the rate constant of softening during subsequent steaming has been evaluated. A response surface two factor interaction model could well describe this effect. Pre-treatments enable more flexibility to optimise several product properties like health, texture and colour. The predictive model presented here is a valuable tool for this multi-criteria optimisation. Industrial relevance A model to describe the softening of vegetable texture during steaming is presented, and the effect of pre-treatment conditions on the reduction of the subsequent softening rate is included in the model. With this model vegetable texture can be improved by predicting the optimal time and temperature of the pre-treatment. This model can be integrated into a multi-criteria optimization approach to improve other quality attributes and still give a desired texture.
    Abscisic acid (ABA) sensitivity regulates desiccation tolerance in germinated Arabidopsis seeds
    Maia de Oliveira, J. ; Dekkers, S.J.W. ; Dolle, M. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
    New Phytologist 203 (2014)1. - ISSN 0028-646X - p. 81 - 93.
    bzip transcription factors - medicago-truncatula seeds - 2c protein phosphatases - signal-transduction - drought tolerance - thaliana - stress - gene - maturation - expression
    During germination, orthodox seeds lose their desiccation tolerance (DT) and become sensitive to extreme drying. Yet, DT can be rescued, in a well-defined developmental window, by the application of a mild osmotic stress before dehydration. A role for abscisic acid (ABA) has been implicated in this stress response and in DT re-establishment. However, the path from the sensing of an osmotic cue and its signaling to DT re-establishment is still largely unknown. Analyses of DT, ABA sensitivity, ABA content and gene expression were performed in desiccation- sensitive (DS) and desiccation-tolerant Arabidopsis thaliana seeds. Furthermore, loss and re-establishment of DT in germinated Arabidopsis seeds was studied in ABA-deficient and ABA-insensitive mutants. We demonstrate that the developmental window in which DT can be re-established correlates strongly with the window in which ABA sensitivity is still present. Using ABA biosynthesis and signaling mutants, we show that this hormone plays a key role in DT re-establishment. Surprisingly, re-establishment of DT depends on the modulation of ABA sensitivity rather than enhanced ABA content. In addition, the evaluation of several ABA-insensitive mutants, which can still produce normal desiccation-tolerant seeds, but are impaired in the re-establishment of DT, shows that the acquisition of DT during seed development is genetically different from its re-establishment during germination.
    Genome-wide analysis of desiccation tolerance-related genes in Arabidopsis seeds
    Maia de Oliveira, Julio ; Dekkers, Bas ; Ligterink, Wilco ; Provart, Nicholas J. ; Hilhorst, Henk - \ 2013
    Wageningen University
    GSE30853 - Arabidopsis thaliana - PRJNA144143 - GSE30853 - Arabidopsis thaliana - PRJNA144143
    The combination of robust physiological models with “omics” studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. Here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (DT) in Arabidopsis thaliana seeds. We show that the incubation of desiccation-sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution re-induces the mechanisms necessary for expression of DT. Based on a SNP-tile array gene expression profile, our data indicates that the re-establishment of DT, in this system, is related to a programmed reversion from a metabolic active to a quiescent state similar to prior to germination. Our findings show that transcripts of germinated seeds after the PEG treatment are dominated by those encoding LEA, seed storage and dormancy-related proteins. On the other hand, a massive repression of genes belonging to many other classes such as photosynthesis, cell wall modification and energy metabolism occurs in parallel. Furthermore, comparison with a similar system for Medicago truncatula reveals a significant overlap between the two transcriptomes. Such overlap may highlight core mechanisms and key regulators of the trait DT. Taking into account the availability of the many genetic and molecular resources for Arabidopsis, the described system may prove useful for unraveling DT in higher plants.
    Arabidopsis seeds as a system to understand desiccation tolerance
    Maia de Oliveira, J. ; Dekkers, S.J.W. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2013
    South African Journal of Botany 86 (2013). - ISSN 0254-6299 - p. 157 - 157.
    Desiccation tolerance (DT) is observed across all biological kingdoms and is a relevant phenomenon in an ecological, social and economic context. In face of imminent climate changes DT will become a highly relevant trait for crop production, as well as for wild plant species conservation. When did desiccation tolerance first appear? How can any organism survive complete drying? What are the structural, molecular, biochemical and genetic principles involved in this phenomenon? Are the mechanisms orchestrating DT conserved among the biological kingdoms? Inspired by these questions and the proven complexity of this trait we have developed an experimental system to re-establish DT in Arabidopsis thaliana seeds. We show that the incubation of desiccation sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution, in exogenous abscisic acid (ABA), or a combination of both, re-activates the mechanisms necessary for expression of DT. By using this model of loss and reestablishment of DT in combination with ABA-deficient and -insensitive mutants, we prove that ABA is necessary for the reestablishment of DT and hypothesize that the events upstream of ABA signaling are not necessary to rescue DT. Furthermore, we demonstrate that ABA sensitivity correlates with the developmental window of the seed/seedling in which DT can be rescued. We also explored this system to investigate the transcriptome, the primary metabolome and the total proteome involved in DT as a first attempt to uncouple osmotic and ABA specific pathways that are regulating this trait.
    Water zuiveren met drijvende planten
    Keizer-Vlek, H.E. ; Verdonschot, P.F.M. ; Verdonschot, R.C.M. ; Dekkers, T.B.M. - \ 2013
    H2O : tijdschrift voor watervoorziening en afvalwaterbehandeling 46 (2013)10. - ISSN 0166-8439 - p. 46 - 47.
    waterzuivering - helofytenfilters - stedelijke gebieden - wetlands - water treatment - artificial wetlands - urban areas - wetlands
    Drijvende moerassystemen met helofyten, ook wel floating treatment wetlands of floatlands genoemd, worden in Nederland uitsluitend toegepast om natuurbeleving te stimuleren en de biodiversiteit van het oppervlaktewater te vergroten. Floatlands zijn echter mogelijk ook geschikt om nutriënten uit het oppervlaktewater te verwijderen. Vooral in het stedelijk gebied is dit een aantrekkelijke optie. De gele lis is er uitermate voor geschikt.
    Similar seasonal peak in clustered and unique extra-pulmonary tuberculosis notifications: winter crowding hypothesis ruled out?
    Top, R. ; Boshuizen, H.C. ; Dekkers, A. - \ 2013
    The International Journal of Tubercolosis and Lung Disease 17 (2013)11. - ISSN 1027-3719 - p. 1466 - 1471.
    vitamin-d deficiency - netherlands - exposure - sunlight
    BACKGROUND: The incidence of extra-pulmonary tuberculosis (EPTB) in the Netherlands shows a seasonal trend, with a peak in spring and a trough in autumn. Possible causes of this peak are winter crowding and a seasonal decrease in immune competence in spring. A third explanation may be a reporting bias. OBJECTIVE: To investigate the role of winter crowding by a time-series analysis of notification data. DNA fingerprinting clustering status can differentiate between recent and remote infections. Seasonality in clustered cases would reflect enhanced transmission in winter and/or seasonally lowered immunity, while seasonality in unique cases would only reflect seasonally lowered immunity. METHODS: We fitted (seasonal) auto-regressive moving average models to culture-positive TB notifications in the Netherlands (1993–2008) to assess seasonality. We then used seasonal trend Loess decompositions to derive the seasonal pattern, and compared the heights of the seasonal peaks. RESULTS: Clustered and unique EPTB notifications showed a seasonal trend that was absent in clustered and unique PTB notifications. The seasonal peak in clustered EPTB cases was not significantly higher than in unique EPTB cases. CONCLUSIONS: The similar timing and height of the seasonal peak of clustered and unique EPTB cases suggests that winter crowding is unlikely to cause the seasonal trend in notifications.
    Dietary modulation of plasma angiopoietin-like protein 4 concentrations in healthy volunteers and in patients with type 2 diabetes
    Jonker, J.T. ; Smit, J.W.A. ; Hammer, S. ; Snel, M. ; Meer, R. van der; Lamb, H.J. ; Mattijssen, F.B.J. ; Mudde, C.M. ; Jazet, I.M. ; Dekkers, O.M. ; Roos, A. de; Romijn, J.A. ; Kersten, A.H. ; Rensen, P.C.N. - \ 2013
    American Journal of Clinical Nutrition 97 (2013)2. - ISSN 0002-9165 - p. 255 - 260.
    myocardial triglyceride content - free fatty-acids - lipoprotein-lipase - caloric restriction - diastolic function - angptl4 - mice - hyperlipidemia - inhibition - humans
    Background: Angiopoietin-like protein 4 (ANGPTL4) has been identified as an inhibitor of lipoprotein lipase. Preliminary data suggest that plasma nonesterified fatty acids (NEFAs) raise plasma ANGPTL4 concentrations in humans. Objective: The objective was to assess plasma ANGPTL4 concentrations after various nutritional interventions that increase NEFA concentrations in healthy subjects and in patients with type 2 diabetes mellitus. Design: We studied 4 groups, both at baseline and after 3 d of either fasting (n = 22 healthy men), a very-low-calorie diet (VLCD; n = 10 healthy men and n = 10 patients with diabetes), or a high-fat, high-energy diet (HFED; n = 15 healthy men). Plasma ANGPTL4, NEFA, and triglyceride concentrations were measured. Results: In healthy men, a VLCD increased ANGPTL4 from 13.2 (IQR: 8.1-24.2) at baseline to 18.2 (16.7-33.4) ng/mL (P <0.05), fasting increased ANGPTL4 from 10.6 (7.6-17.6) to 28.0 (23.1-35.0) ng/mL (P <0.05), and an HFED increased ANGPTL4 from 13.9 (8.2-22.0) to 17.2 (11.2-23.6) ng/mL (P <0.05). In men with diabetes, a VLCD also increased ANGPTL4, from 10.9 +/- 2.4 to 19.2 +/- 3.2 ng/mL (P <0.05). All interventions significantly increased plasma NEFAs in both healthy men and patients with diabetes. The change in ANGPTL4 positively correlated with the change in NEFA concentrations (beta = 0.048, P <0.001) and negatively correlated with the change in plasma triglycerides (beta = -0.051, P = 0.01). Conclusions: Three days of either fasting, a VLCD, or an HFED increased plasma ANGPTL4 concentrations in healthy men, concomitantly with increased plasma NEFA concentrations. Similarly, a VLCD in patients with diabetes increased ANGPTL4 concentrations, concomitantly with increased NEFA concentrations. Am J Clin Nutr 2013;97:255-60.
    Aquatische Oligochaeta (Bijdrage aan reader voor determinatiecursus van Alterra, 2013-10-28/2013-10-29)
    Dekkers, Dorine - \ 2013
    Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination
    Dekkers, S.J.W. ; Pearce, S. ; Bolderen-Veldkamp, R.P. ; Marshall, A. ; Widera, P. ; Gilbert, J. ; Drost, H.G. ; Bassel, G. ; Muller, K. ; King, J.R. ; Wood, A. ; Grosse, I. ; Bentsink, L. - \ 2013
    Plant Physiology 163 (2013)1. - ISSN 0032-0889 - p. 205 - 215.
    thaliana seeds - abscisic-acid - leaf senescence - gene activity - endosperm - reveals - dormancy - metabolism - embryo - touch
    Seed germination is a critical stage in the plant life cycle and the first step toward successful plant establishment. Therefore, understanding germination is of important ecological and agronomical relevance. Previous research revealed that different seed compartments (testa, endosperm, and embryo) control germination, but little is known about the underlying spatial and temporal transcriptome changes that lead to seed germination. We analyzed genome-wide expression in germinating Arabidopsis (Arabidopsis thaliana) seeds with both temporal and spatial detail and provide Web-accessible visualizations of the data reported (vseed.nottingham.ac.uk). We show the potential of this high-resolution data set for the construction of meaningful coexpression networks, which provide insight into the genetic control of germination. The data set reveals two transcriptional phases during germination that are separated by testa rupture. The first phase is marked by large transcriptome changes as the seed switches from a dry, quiescent state to a hydrated and active state. At the end of this first transcriptional phase, the number of differentially expressed genes between consecutive time points drops. This increases again at testa rupture, the start of the second transcriptional phase. Transcriptome data indicate a role for mechano-induced signaling at this stage and subsequently highlight the fates of the endosperm and radicle: senescence and growth, respectively. Finally, using a phylotranscriptomic approach, we show that expression levels of evolutionarily young genes drop during the first transcriptional phase and increase during the second phase. Evolutionarily old genes show an opposite pattern, suggesting a more conserved transcriptome prior to the completion of germination.
    Nutrient removal capacity of floating treatment wetlands
    Vlek, H.E. ; Verdonschot, R.C.M. ; Verdonschot, P.F.M. ; Dekkers, T.B.M. - \ 2013
    Floatlands veelbelovend als waterzuiveraar in stadswateren
    Vlek, H.E. ; Verdonschot, R.C.M. ; Verdonschot, P.F.M. ; Dekkers, T.B.M. - \ 2013
    H2O online juli 2013 (2013).
    waterzuivering - helofytenfilters - stedelijke gebieden - wetlands - water treatment - artificial wetlands - urban areas - wetlands
    Drijvende moerassystemen met helofyten, ook wel floating treatment wetlands of floatlands genoemd, worden in Nederland uitsluitend toegepast om natuurbeleving te stimuleren en de biodiversiteit van het oppervlaktewater te vergroten. Floatlands zijn echter mogelijk ook geschikt om nutriënten uit het oppervlaktewater te verwijderen. Vooral in het stedelijk gebied is dit een aantrekkelijke optie.
    Evaluation of food and nutrient intake assessment using concentration biomarkers in European adolescents from the Healthy Lifestyle in Europe by Nutrition in Adolescence study
    Vandevijvere, S. ; Geelen, A. ; Gonzalez-Gross, M. ; Veer, P. van 't; Dallongeville, J. ; Mouratidu, T. ; Dekkers, A. ; Börnhorst, C. ; Breidenassel, C. - \ 2013
    The British journal of nutrition 109 (2013)4. - ISSN 0007-1145 - p. 736 - 747.
    serum cholesteryl esters - n-3 fatty-acids - dietary-intake - energy-intake - additional measurements - micronutrient intake - biochemical markers - adipose-tissue - vitamin-c - validation
    Accurate food and nutrient intake assessment is essential for investigating diet–disease relationships. In the present study, food and nutrient intake assessment among European adolescents using 24 h recalls (mean of two recalls) and a FFQ (separately and the combination of both) were evaluated using concentration biomarkers. Biomarkers included were vitamin C, ß-carotene, DHA+EPA, vitamin B12 (cobalamin and holo-transcobalamin) and folate (erythrocyte folate and plasma folate). For the evaluation of the food intake assessment 390 adolescents were included, while 697 were included for the nutrient intake assessment evaluation. Spearman rank and Pearson correlations, and validity coefficients, which are correlations between intake estimated and habitual true intake, were calculated. Correlations were higher between frequency of food consumption (from the FFQ) and concentration biomarkers than between mean food intake (from the recalls) and concentration biomarkers, especially for DHA+EPA (r 0·35 v. r 0·27). Most correlations were higher among girls than boys. For boys, the highest validity coefficients were found for frequency of fruit consumption (0·88) and for DHA+EPA biomarker (0·71). In girls, the highest validity coefficients were found for fruit consumption frequency (0·76), vegetable consumption frequency (0·74), mean fruit intake (0·90) and DHA+EPA biomarker (0·69). After exclusion of underreporters, correlations slightly improved. Correlations between usual food intakes, adjusted for food consumption frequency, and concentration biomarkers were higher than correlations between mean food intakes and concentration biomarkers. In conclusion, two non-consecutive 24 h recalls in combination with a FFQ seem to be appropriate to rank subjects according to their usual food intake
    Metagenomics of the rhizosphere microbiome to identify disease suppressive bacteria
    Mendes, R. ; Kruijt, M. ; Bruijn, I. de; Dekkers, E. ; Voort, M. van der; Schneider, J.H.M. ; Piceno, Y.M. ; DeSantis, T.Z. ; Andersen, G.L. ; Bakker, P.A.H.M. ; Raaijmakers, J.M. - \ 2013
    In: Book of Abstracts 10th International Congress of Plant Pathology, Beijing, China, 25-30 August 2013. - - p. 509 - 509.
    Disease-suppressive soils are exceptional ecosystems in which beneficial microorganisms effectively guard plants against soil-borne pathogen infections. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in disease suppression are not known. To identify such disease-suppressive microbes, PhyloChip-based metagenomics of the rhizosphere microbiome was performed and coupled with culture-dependent functional analyses to identify bacterial taxa and mechanisms involved in soil suppressiveness to the fungal root pathogen Rhizoctonia solani. The PhyloChip analyses led to the identification of more than 30,000 bacterial and archaeal taxa from soils with different levels of disease suppressiveness. The results of these analyses specifically pointed to the Proteobacteria, Firmicutes and Actinobacteria as the most dynamic groups associated with disease suppression. Although the richness of these bacterial taxa was not significantly different between suppressive and conducive soils, their relative abundance correlated well with the different levels of disease suppressiveness. Targeted isolation and functional analyses led to the identification of specific members of the ¿-Proteobacteria with in vitro and in situ activity against Rhizoctonia solani. In conclusion, this study provides new insights into rhizobacterial diversity and fundamental mechanisms underlying multi-trophic interactions in natural disease suppressive soils.
    Door de bomen het bos weer zien, 6e Nederlandse bosinventarisatie levert schat aan informatie
    Schelhaas, M.J. ; Dekkers, R. - \ 2013
    Vakblad Natuur Bos Landschap 5 (2013)10. - ISSN 1572-7610 - p. 14 - 17.
    bosecologie - bossen - bosbeheer - inventarisaties - forest ecology - forests - forest administration - inventories
    Binnen een jaar tijd doen zes veldwerkers metingen aan zo’n 70.000 bomen op 3.745 steekproefpunten in heel Nederland. Dat gebeurt in het kader van de 6e Nederlandse Bosinventarisatie, die Alterra in opdracht van het ministerie van Economische Zaken coördineert. Begin 2014 komen de data beschikbaar voor de bos- en natuursector. Wat gebeurt er eigenlijk met de data en wat kan de sector met de resultaten?
    Knowledge gaps in risk assessment of nanosilica in food: evaluation of the dissolution and toxicity of different forms of silica
    Dekkers, S. ; Bouwmeester, H. ; Bos, P.M.J. ; Peters, R.J.B. ; Rietveld, A. ; Oomen, A.G. - \ 2013
    Nanotoxicology 7 (2013)4. - ISSN 1743-5390 - p. 367 - 377.
    in-vivo biodistribution - tissue distribution - urinary-excretion - nanoparticles - size - mice - clearance
    This manuscript describes the follow-up study of our previous publication on the presence and risks of nanosilica in food. New information on the presence of nanosilica in the gastrointestinal tract is evaluated and information on nanosilica and synthetic amorphous silica (SAS) is compared to assess its relevance for risk assessment of nanosilica in food. Irrespective of whether SAS should be regarded as a nanomaterial or a non-nanoform of silica, a comparison to nanosilica is relevant to determine whether there are differences in physicochemical properties, which may lead to differences in toxicity. Based on this comparison, knowledge gaps are identified and recommendations for a targeted approach to facilitate risk assessment of nanosilica in food are given. Considering the discussion to which extent nanomaterials with (slightly) different physicochemical characteristics can be grouped for risk assessment - the sameness issue - actual exercises as presented in this manuscript are highly relevant for bringing this discussion forward.
    Unravelling hazards of nanoparticles to earthworms, from gene to population
    Ploeg, M. van der - \ 2013
    Wageningen University. Promotor(en): Ivonne Rietjens, co-promotor(en): Nico van den Brink. - S.l. : s.n. - ISBN 9789461734440 - 192
    aardwormen - lumbricus rubellus - nanotechnologie - blootstelling - ecotoxicologie - earthworms - lumbricus rubellus - nanotechnology - exposure - ecotoxicology

    Nanotechnology is an expeditiously growing field, where engineered nanoparticles are being incorporated in many different applications, from food to waste water treatment (Dekkers et al. 2011; Gottschalk and Nowack 2011; Savage and Diallo 2005). Due to this large scale production and use of nanoparticles, their release into the environment seems inevitable (Crane et al. 2008; Handy et al. 2008a; Oberdörster et al. 2005). Actual exposure levels of nanoparticles under field conditions and the hazards of nanoparticle exposure to the environment are poorly understood, especially for the soil environment (Kahru and Dubourguier 2010; Navarro et al. 2008; Shoults-Wilson et al. 2011a).

    Given the need for better characterization of hazards of engineered nanoparticles to the environment and soil organisms in particular, the aim of the present thesis was to investigate effects of nanoparticle exposure on the earthworm Lumbricus rubellus, as a model organism for soil ecotoxicology, and to contribute to the development of effect markers for engineered nanoparticle exposure in this model.

    The present thesis was divided in different chapters. Chapter 1 provides an introduction to the topic and discusses the importance of research on the hazards of exposure to engineered nanoparticles. Furthermore, the aim and outline of the thesis are presented, with background information on the model organism, effect markers and nanoparticles.

    In chapter 2 effects of exposure to the fullerene C60 (nominal concentrations 0, 15.4 and 154 mg C60/kg soil) on survival and growth during the different life stages of L. rubellus (cocoon, juvenile, subadult and adult), as well as reproduction were quantified. These important individual endpoints for population dynamics were incorporated in a continuous-time life-history model (Baveco and De Roos 1996; De Roos 2008). In this way, effects of C60 exposure on the individual endpoints could be extrapolated to implications for population growth rate and life stage distribution, i.e. the development of the population in terms of number of individuals in the different life stages. These implications at the population level may be more relevant for the ecological impact of C60 than effects on endpoints at the individual level (Klok et al. 2006; Widarto et al. 2004). At the individual level C60 exposure caused significant adverse effects on cocoon production, juvenile growth rate and survival. When these endpoints were used to model effects on the population level, reduced population growth rates with increasing C60 concentrations were observed. Furthermore, a shift in life stage structure was shown for C60 exposed populations, towards a larger proportion of juveniles. This result implies that the lower juvenile growth rate induced by C60 exposure resulted in a larger proportion of juveniles, despite increased mortality among juveniles. Overall, this study implied serious consequences of C60 exposure for L. rubellus earthworm populations, even at the lowest level of exposure tested. Furthermore, it showed that juveniles were more sensitive to C60 exposure than adults.

    To complement the observations made on survival, growth and reproduction described in chapter 2, subsequent investigations on cellular and molecular responses of the earthworms to C60 exposure were performed (chapter 3). A set of established effect markers was used, which reflect different levels of biological organisation in the earthworm and may inform on the toxic mechanisms of adverse effects induced by C60 exposure (Handy et al. 2002; Heckmann et al. 2008). At the molecular level, four specific effect markers were selected, including markers for generic stress (heat shock protein 70 (HSP70) (van Straalen and Roelofs 2006), for oxidative stress (catalase and glutathione-S-transferase (GST) (Kohen and Nyska 2002) and for an immune response (coelomic cytolytic factor-1 (CCF-1) (Olivares Fontt et al. 2002). At the tissue level, histological analyses were used to identify damage to cells and tissues, and indications of inflammation in the tissues. In these investigations, exposure to C60 (0, 15 or 154 mg C60/kg soil) affected gene expression of HSP70 significantly. Gene expression of CCF-1 did not alter in adult earthworms exposed for four weeks, but was significantly down-regulated after lifelong exposure (from cocoon stage to adulthood) of earthworms, already to the lowest C60 exposure level. No significant trends were noted for catalase and glutathione-S-transferase (GST) gene expression or enzyme activity. Tissue samples of the C60 exposed earthworms from both experiments and exposure levels, showed a damaged cuticle with underlying pathologies of epidermis and muscles. Additionally, the gut barrier was not fully intact. However, tissue repair was also observed in these earthworms. In conclusion, this study demonstrated effects of sub-lethal C60 exposure on L. rubellus earthworms, at the level of gene expression and tissue integrity.

    Although tissue injury is generally associated with an inflammatory response, as part of tissue repair (Cikutovic et al. 1999; Goven et al. 1994), the tissue damage observed for the in vivo C60 exposed earthworms in chapter 3 appeareded to occur without accompanying induced immune responses. The CCF-1 gene expression level was reduced in the C60 exposed earthworms, and histological observations did not show infiltration of damaged tissues by immune cells. In order to obtain further insight in mechanisms of effects observed at the molecular and tissue level on immune related parameters, the sensitivity of immune cells (coelomocytes) of L. rubellus earthworms towards exposure to selected nanoparticles was investigated in vitro (chapter 4). To this end, coelomocytes were isolated from unexposed adult L. rubellus earthworms and exposed to C60 in vitro. After exposure, these coelomocytes were tested for cellular viability, phagocytic activity and CCF-1 gene expression levels. The gene expression of CCF-1 was most affected, demonstrating a strong reduction, which indicated immunosuppression. Experiments with NR8383 rat macrophage cells and tri-block copolymer nanoparticles were used to compare sensitivity of the cell types and showed the usefulness of coelomocytes as a test system for nano-immunotoxicity in general. Overall, this study indicated that the absence of an immune response, in case of tissue injuries observed after in vivo C60 exposure, is likely caused by immunosuppression rather than coelomocyte mortality.

    In subsequent investigations, the experiments performed for C60 were also carried out with silver nanoparticles (AgNP), both in vivo and in vitro (chapter 5). Effects of AgNP were assessed in vivo at nominal concentrations of 0, 1.5 (low), 15.4 (medium) and 154 (high) mg Ag/kg soil and compared to effects of silver ions, added as AgNO3 (nominal concentration 15.4 mg Ag/kg soil). In a four week reproduction assay, the high AgNP and AgNO3 treatments had a significant effect on cocoon production and high AgNP exposure also caused a reduction in weight gain of the adult earthworms. No juveniles survived the high AgNP treatment, therefore only F1 earthworms from the other exposure treatments were monitored for survival and growth, until adulthood. These individual endpoints were used to model effects on the population level. The low and medium AgNP as well as the AgNO3 treatments significantly reduced the population growth rate. The high AgNP treatment caused complete failure of the population growth. Furthermore, histological examination of the earthworms from all AgNP exposure treatments demonstrated tissue damage, with injuries mainly at the external barriers, e.g. the cuticle and the gut epithelium. In addition, effects of AgNP exposure were assessed in vitro and a reduction of coelomocyte viability was observed in a concentration-dependent manner, although the EC50 was fourteen times higher compared with that for Ag ions, added as AgNO3. Furthermore, characterisation of the in vivo exposure media implied that AgNP remained present in the soil in single and aggregated state, releasing Ag to the soil pore water up to at least eleven months. The ionic fraction of Ag in soils has been suggested to be bioavailable to organisms and (largely) responsible for the observed AgNP toxicity (Coutris et al. 2012; Koo, et al. 2011; Shoults-Wilson et al. 2011b). In comparison, the AgNO3 seemed to dissolve rapidly, as is also known for this metal salt, and fixation of Ag ions by the soil presumably led to a quick reduction of Ag bioavailability (Atkins and Jones 2000; Coutris et al. 2012; Ratte 1999). This is in line with the observation that effects were more prolonged in the AgNP treatments in comparison with the AgNO3 exposed animals. In conclusion, this study indicated that AgNP exposure may seriously affect earthworm populations, with the ability to cause immunotoxicity, injury to the external barriers of the earthworm body and a reduction in growth, reproduction and juvenile survival.

    Finally, chapter 6 presents a discussion on the findings of the present thesis and provides suggestions for future research.

    Interview Muggen-monitoring in de Onlanden
    Dekkers, Dorine - \ 2012
    Odonata exuvien/larven
    Dekkers, T.B.M. ; Brochard, C. ; Lohr, M. ; Martens, A. - \ 2012
    Wageningen : Alterra
    Letter to the Editor : Nanosilica? Clarifications are necessary! Response to Bosch et al.
    Dekkers, S. ; Krystek, P. ; Peters, R.J.B. ; Lankveld, D.P.K. ; Bokkers, B.G.H. ; Hoeven-Arentzen, P.H. van; Bouwmeester, H. ; Oomen, A.G. - \ 2012
    Nanotoxicology 6 (2012). - ISSN 1743-5390 - p. 612 - 613.
    Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands
    Schurink, A. ; Wolc, A. ; Ducro, B.J. ; Frankena, K. ; Garrick, D.J. ; Dekkers, J.C.M. ; Arendonk, J.A.M. van - \ 2012
    Genetics, Selection, Evolution 44 (2012)1. - ISSN 0999-193X - 12 p.
    icelandic horses - linkage disequilibrium - summer eczema - bayesian-inference - allergic diseases - sequence - polymorphisms - prediction - genetics - vector
    Background: Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about genes contributing to the genetic variance associated with insect bite hypersensitivity. Therefore, the aim of our study was to identify and quantify genomic associations with insect bite hypersensitivity in Shetland pony mares and Icelandic horses in the Netherlands. Methods: Data on 200 Shetland pony mares and 146 Icelandic horses were collected according to a matched case–control design. Cases and controls were matched on various factors (e.g. region, sire) to minimize effects of population stratification. Breed-specific genome-wide association studies were performed using 70 k single nucleotide polymorphisms genotypes. Bayesian variable selection method Bayes-C with a threshold model implemented in GenSel software was applied. A 1 Mb non-overlapping window approach that accumulated contributions of adjacent single nucleotide polymorphisms was used to identify associated genomic regions. Results: The percentage of variance explained by all single nucleotide polymorphisms was 13% in Shetland pony mares and 28% in Icelandic horses. The 20 non-overlapping windows explaining the largest percentages of geneticvariance were found on nine chromosomes in Shetland pony mares and on 14 chromosomes in Icelandic horses. Overlap in identified associated genomic regions between breeds would suggest interesting candidate regions to follow-up on. Such regions common to both breeds (within 15 Mb) were found on chromosomes 3, 7, 11, 20 and 23. Positional candidate genes within 2 Mb from the associated windows were identified on chromosome 20 in both breeds. Candidate genes are within the equine lymphocyte antigen class II region, which evokes an immune response by recognizing many foreign molecules. Conclusions: The genome-wide association study identified several genomic regions associated with insect bite hypersensitivity in Shetland pony mares and Icelandic horses. On chromosome 20, associated genomic regions in both breeds were within 2 Mb from the equine lymphocyte antigen class II region. Increased knowledge on insect bite hypersensitivity associated genes will contribute to our understanding of its biology, enabling more efficient selection, therapy and prevention to decrease insect bite hypersensitivity prevalence.
    Distinct cell wall architectures in seed endosperms in representatives of the brassicaceae and solanaceae
    Lee, K.J.D. ; Dekkers, S.J.W. ; Steinbercher, T. ; Walsh, C.T. ; Bacic, T. ; Bentsink, L. ; Leubner-Metzger, G. ; Knox, J.P. - \ 2012
    Plant Physiology 160 (2012)3. - ISSN 0032-0889 - p. 1551 - 1566.
    cellulose synthase-like - hydroxyproline-rich glycoprotein - arabidopsis-thaliana - abscisic-acid - lepidium-sativum - micropylar endosperm - monoclonal-antibody - elongation growth - hydroxyl radicals - mannanase activity
    In some species, a crucial role has been demonstrated for the seed endosperm during germination. The endosperm has been shown to integrate environmental cues with hormonal networks that underpin dormancy and seed germination, a process that involves the action of cell wall remodeling enzymes (CWREs). Here, we examine the cell wall architectures of the endosperms of two related Brassicaceae, Arabidopsis (Arabidopsis thaliana) and the close relative Lepidium (Lepidium sativum), and that of the Solanaceous species, tobacco (Nicotiana tabacum). The Brassicaceae species have a similar cell wall architecture that is rich in pectic homogalacturonan, arabinan, and xyloglucan. Distinctive features of the tobacco endosperm that are absent in the Brassicaceae representatives are major tissue asymmetries in cell wall structural components that reflect the future site of radicle emergence and abundant heteromannan. Cell wall architecture of the micropylar endosperm of tobacco seeds has structural components similar to those seen in Arabidopsis and Lepidium endosperms. In situ and biomechanical analyses were used to study changes in endosperms during seed germination and suggest a role for mannan degradation in tobacco. In the case of the Brassicaceae representatives, the structurally homogeneous cell walls of the endosperm can be acted on by spatially regulated CWRE expression. Genetic manipulations of cell wall components present in the Arabidopsis seed endosperm demonstrate the impact of cell wall architectural changes on germination kinetics.
    Mobility of lowland stream trichoptera under experimental habitat and flow conditions
    Verdonschot, P.F.M. ; Besse, A.A. ; Dekkers, T.B.M. ; Verdonschot, R.C.M. - \ 2012
    Limnologica 42 (2012)3. - ISSN 0075-9511 - p. 227 - 234.
    benthic invertebrates - field experiments - upstream movements - running waters - river systems - drift - colonization - community - patterns - behavior
    The species-specific mobility of six species of lowland stream Trichoptera was studied in flume experiments with different habitats and current flows. The test species were selected according to their occurrence along the environmental gradient from more natural towards highly disturbed sandy, lowland streams of the North-West European plain. Two groups of species were distinguished, three species occurring more frequently towards the natural end versus three occurring more frequently towards the disturbed end of the stream disturbance gradient. Experiments were conducted in a temperature and light controlled environment in indoor, re-circulating, man-made stream channels with four replicate gutters each. The bottom of each gutter held ten trays filled with five selected habitat materials (two trays each), which provided refugia and food. Three flow treatments with constant current velocities of 10, 30, or 50 cm/s were applied. Movements were scored based on visual observations of the position of each individual at fixed time points. The first day after release, individuals moved around very actively; this ‘release effect’ was removed from further analyses. The trichopteran species occurring near the more natural end of the disturbance gradient exhibited significantly less mobility (on average 10–15% of individuals actively moved around) than the species from the more disturbed end of the gradient (on average 30–40% of individuals actively moved around). The first group of trichopteran species also spent significantly longer times in the leaves habitat compared to the other three species, which moved more or less independent of habitat. With increasing current velocity, all test species moved more frequently, particularly the species from the more disturbed end of the gradient. This could indicate behavior to avoid dislodgement. The mobility of all species exceeded the mobility needed to use habitat resources of food and shelter, both present in excess. Therefore, short-term movement could also be (partly) a random behavior. Overall, the more tolerant species from the disturbed end of the gradient showed more mobility and flexibility than the species occurring under more or less natural stream conditions. This was consistent with the hypothesis that mobility is an adaptation of tolerant, ubiquitous species. Mobility is an adaptation of r-strategists.
    Metabolic and transcriptomic changes induced in Arabidopsis by the rhizobacterium Pseudomonas fluorescens SS101
    Mortel, J.E. van de; Vos, R.C.H. de; Dekkers, E. ; Pineda, A. ; Guillod, L. ; Bouwmeester, K. ; Loon, J.J.A. van; Dicke, M. ; Raaijmakers, J.M. - \ 2012
    Plant Physiology 160 (2012)4. - ISSN 0032-0889 - p. 2173 - 2188.
    induced systemic resistance - growth-promoting rhizobacteria - tobacco necrosis virus - syringae pv. tomato - salicylic-acid - acquired-resistance - aeruginosa 7nsk2 - gene-expression - beneficial microbes - disease resistance
    Systemic resistance induced in plants by nonpathogenic rhizobacteria is typically effective against multiple pathogens. Here, we show that root-colonizing Pseudomonas fluorescens strain SS101 (Pf.SS101) enhanced resistance in Arabidopsis (Arabidopsis thaliana) against several bacterial pathogens, including Pseudomonas syringae pv tomato (Pst) and the insect pest Spodoptera exigua. Transcriptomic analysis and bioassays with specific Arabidopsis mutants revealed that, unlike many other rhizobacteria, the Pf.SS101-induced resistance response to Pst is dependent on salicylic acid signaling and not on jasmonic acid and ethylene signaling. Genome-wide transcriptomic and untargeted metabolomic analyses showed that in roots and leaves of Arabidopsis plants treated with Pf.SS101, approximately 1,910 genes and 50 metabolites were differentially regulated relative to untreated plants. Integration of both sets of “omics” data pointed to a prominent role of camalexin and glucosinolates in the Pf.SS101-induced resistance response. Subsequent bioassays with seven Arabidopsis mutants (myb51, cyp79B2cyp79B3, cyp81F2, pen2, cyp71A12, cyp71A13, and myb28myb29) disrupted in the biosynthesis pathways for these plant secondary metabolites showed that camalexin and glucosinolates are indeed required for the induction of Pst resistance by Pf.SS101. Also for the insect S. exigua, the indolic glucosinolates appeared to play a role in the Pf.SS101-induced resistance response. This study provides, to our knowledge for the first time, insight into the substantial biochemical and temporal transcriptional changes in Arabidopsis associated with the salicylic acid-dependent resistance response induced by specific rhizobacteria.
    Identification of Reference Genes For RT-qPCR Expression Analysis In Arabidopsis And Tomato Seeds
    Dekkers, S.J.W. ; Willems, L.A.J. ; Bassel, G. ; Bolderen-Veldkamp, R.P. van; Ligterink, W. ; Hilhorst, H.W.M. ; Bentsink, L. - \ 2012
    Plant and Cell Physiology 53 (2012)1. - ISSN 0032-0781 - p. 28 - 37.
    quantitative pcr data - real-time pcr - gibberellin biosynthesis - housekeeping genes - low-temperature - messenger-rna - abscisic-acid - data sets - germination - normalization
    Quantifying gene expression levels is an important research tool to understand biological systems. Reverse transcription–quantitative real-time PCR (RT–qPCR) is the preferred method for targeted gene expression measurements because of its sensitivity and reproducibility. However, normalization, necessary to correct for sample input and reverse transcriptase efficiency, is a crucial step to obtain reliable RT–qPCR results. Stably expressed genes (i.e. genes whose expression is not affected by the treatment or developmental stage under study) are indispensable for accurate normalization of RT–qPCR experiments. Lack of accurate normalization could affect the results and may lead to false conclusions. Since transcriptomes of seeds are different from other plant tissues, we aimed to identify reference genes specifically for RT–qPCR analyses in seeds of two important seed model species, i.e. Arabidopsis and tomato. We mined Arabidopsis seed microarray data to identify stably expressed genes and analyzed these together with putative reference genes from other sources. In total, the expression stability of 24 putative reference genes was validated by RT–qPCR in Arabidopsis seed samples. For tomato, we lacked transcriptome data sets of seeds and therefore we tested the tomato homologs of the reference genes found for Arabidopsis seeds. In conclusion, we identified 14 Arabidopsis and nine tomato reference genes. This provides a valuable resource for accurate normalization of gene expression experiments in seed research for two important seed model species.
    A comparison by simulation of different methods to estimate the usual intake distribution for episodically consumed foods.
    Goedhart, P.W. ; Voet, Hilko van der; Knüppel, S. ; Dekkers, A.L.M. ; Dodd, K.W. ; Boeing, H. ; Klaveren, J.D. van - \ 2012
    Parma : EFSA (Supporting Publication 2012:EN-299) - 65 p.
    Predicting urinary creatinine excretion and its usefulness to identify incomplete 24h urine collections
    Keyzer, W. de; Huybrechts, I. ; Dekkers, A.L.M. ; Geelen, A. ; Crispim, S.P. ; Hulshof, P.J.M. ; Andersen, L.F. ; Rehurkova, I. ; Ruprich, J. ; Volatier, J.L. ; Maele, G. van; Slimani, N. ; Veer, P. van 't; Boer, E. de; Henauw, S. de - \ 2012
    The British journal of nutrition 108 (2012)6. - ISSN 0007-1145 - p. 1118 - 1125.
    4-aminobenzoic acid - european centers - completeness - potassium - diet - validation - stability - recalls - protein - sodium
    Studies using 24 h urine collections need to incorporate ways to validate the completeness of the urine samples. Models to predict urinary creatinine excretion (UCE) have been developed for this purpose; however, information on their usefulness to identify incomplete urine collections is limited. We aimed to develop a model for predicting UCE and to assess the performance of a creatinine index using para-aminobenzoic acid (PABA) as a reference. Data were taken from the European Food Consumption Validation study comprising two non-consecutive 24 h urine collections from 600 subjects in five European countries. Data from one collection were used to build a multiple linear regression model to predict UCE, and data from the other collection were used for performance testing of a creatinine index-based strategy to identify incomplete collections. Multiple linear regression (n 458) of UCE showed a significant positive association for body weight (ß = 0·07), the interaction term sex × weight (ß = 0·09, reference women) and protein intake (ß = 0·02). A significant negative association was found for age (ß = - 0·09) and sex (ß = - 3·14, reference women). An index of observed-to-predicted creatinine resulted in a sensitivity to identify incomplete collections of 0·06 (95 % CI 0·01, 0·20) and 0·11 (95 % CI 0·03, 0·22) in men and women, respectively. Specificity was 0·97 (95 % CI 0·97, 0·98) in men and 0·98 (95 % CI 0·98, 0·99) in women. The present study shows that UCE can be predicted from weight, age and sex. However, the results revealed that a creatinine index based on these predictions is not sufficiently sensitive to exclude incomplete 24 h urine collections.
    Tussenstand resultaten vliegexperiment steekmuggen
    Verdonschot, Piet ; Besse-Lototskaya, Anna ; Dekkers, Dorine - \ 2011
    Hydracarina
    Dekkers, Dorine - \ 2011
    The Re-Establishment of Desiccation Tolerance in Germinated Arabidopsis thaliana Seeds and Its Associated Transcriptome
    Maia de Oliveira, J. ; Dekkers, S.J.W. ; Provart, N.J. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2011
    PLoS ONE 6 (2011)12. - ISSN 1932-6203 - 11 p.
    medicago-truncatula seeds - metabolic pathways - gene-expression - somatic embryos - hybridization - mechanisms - induction - resource - genomics - radicles
    The combination of robust physiological models with “omics” studies holds promise for the discovery of genes and pathways linked to how organisms deal with drying. Here we used a transcriptomics approach in combination with an in vivo physiological model of re-establishment of desiccation tolerance (DT) in Arabidopsis thaliana seeds. We show that the incubation of desiccation sensitive (DS) germinated Arabidopsis seeds in a polyethylene glycol (PEG) solution re-induces the mechanisms necessary for expression of DT. Based on a SNP-tile array gene expression profile, our data indicates that the re-establishment of DT, in this system, is related to a programmed reversion from a metabolic active to a quiescent state similar to prior to germination. Our findings show that transcripts of germinated seeds after the PEG-treatment are dominated by those encoding LEA, seed storage and dormancy related proteins. On the other hand, a massive repression of genes belonging to many other classes such as photosynthesis, cell wall modification and energy metabolism occurs in parallel. Furthermore, comparison with a similar system for Medicago truncatula reveals a significant overlap between the two transcriptomes. Such overlap may highlight core mechanisms and key regulators of the trait DT. Taking into account the availability of the many genetic and molecular resources for Arabidopsis, the described system may prove useful for unraveling DT in higher plants
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