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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Managing the hard-to-cook (HTC) phenomenon in bambara groundnut (Vigna subterranea (L.) Verdc.) processing for resource limited communities in Zimbabwe
Mubaiwa, Juliet - \ 2018
Wageningen University. Promotor(en): Vincenzo Fogliano, co-promotor(en): Anita Linnemann. - Wageningen : Wageningen University - ISBN 9789463433556 - 250
Targeting microbial pathogens
Thomma, Bart P.H.J. ; Cook, David E. - \ 2018
Science 360 (2018)6393. - ISSN 0036-8075 - p. 1070 - 1071.
One of the most important challenges in agricultural production is to safeguard crops from pathogen infection. Uncovering the molecular mechanisms governing plant-microbe interactions can provide new strategies by which to sustainably intensify agriculture and can additionally contribute to our broader understanding of interspecies interactions (1). On page 1126 of this issue, Cai et al. (2) report that plant hosts secrete extracellular vesicles containing small RNA (sRNA), which are taken up by, and lead to silencing of, fungal virulence–related genes during infection (see the figure). These findings address the previously unknown phenomenon by which host sRNA can alter gene expression in other organisms, highlighting the role of extracellular vesicle–mediated transport as a key element of cross-kingdom RNA interference (RNAi). This could be exploited in the development of RNAi-based pathogen control strategies to protect crops.
Priorities for protected area research
Dudley, Nigel ; Hockings, Marc ; Stolton, Sue ; Amend, Thora ; Badola, Ruchi ; Bianco, Mariasole ; Chettri, Nakul ; Cook, Carly ; Day, Jon C. ; Dearden, Phil ; Edwards, Mary ; Ferraro, Paul ; Foden, Wendy ; Gambino, Roberto ; Gaston, Kevin J. ; Hayward, Natalie ; Hickey, Valerie ; Irving, Jason ; Jeffries, Bruce ; Karapetyan, Areg ; Kettunen, Marianne ; Laestadius, Lars ; Laffoley, Dan ; Lham, Dechen ; Lichtenstein, Gabriela ; Makombo, John ; Marshall, Nina ; McGeoch, Melodie ; Nguyen, Dao ; Nogué, Sandra ; Paxton, Midori ; Rao, Madhu ; Reichelt, Russell ; Rivas, Jorge ; Roux, Dirk ; Rutte, Claudia ; Schreckenberg, Kate ; Sovinc, Andrej ; Sutyrina, Svetlana ; Utomo, Agus ; Vallauri, Daniel ; Vedeld, Pål Olav ; Verschuuren, Bas ; Waithaka, John ; Woodley, Stephen ; Wyborn, Carina ; Zhang, Yan - \ 2018
PARKS: the International of Protected Areas and Conservation 24 (2018)1. - ISSN 0960-233X - p. 35 - 50.
Managers - Protected areas - Research priorities - Researchers - Stakeholder assessment

A hundred research priorities of critical importance to protected area management were identified by a targeted survey of conservation professionals; half researchers and half practitioners. Respondents were selected to represent a range of disciplines, every continent except Antarctica and roughly equal numbers of men and women. The results analysed thematically and grouped as potential research topics as by both practitioners and researchers. Priority research gaps reveal a high interest to demonstrate the role of protected areas within a broader discussion about sustainable futures and if and how protected areas can address a range of conservation and socio-economic challenges effectively. The paper lists the hundred priorities structured under broad headings of management, ecology, governance and social (including political and economic issues) and helps contribute to setting future research agendas.

Growth of wormlike micelles in nonionic surfactant solutions : Quantitative theory vs. experiment
Danov, Krassimir D. ; Kralchevsky, Peter A. ; Stoyanov, Simeon D. ; Cook, Joanne L. ; Stott, Ian P. ; Pelan, Eddie G. - \ 2018
Advances in Colloid and Interface Science 256 (2018). - ISSN 0001-8686 - p. 1 - 22.
Micelle free energy - Micelle growth - Nonionic surfactants - Polyoxyethylene alkyl ethers - Wormlike micelles
Despite the considerable advances of molecular-thermodynamic theory of micelle growth, agreement between theory and experiment has been achieved only in isolated cases. A general theory that can provide self-consistent quantitative description of the growth of wormlike micelles in mixed surfactant solutions, including the experimentally observed high peaks in viscosity and aggregation number, is still missing. As a step toward the creation of such theory, here we consider the simplest system – nonionic wormlike surfactant micelles from polyoxyethylene alkyl ethers, CiEj. Our goal is to construct a molecular-thermodynamic model that is in agreement with the available experimental data. For this goal, we systematized data for the micelle mean mass aggregation number, from which the micelle growth parameter was determined at various temperatures. None of the available models can give a quantitative description of these data. We constructed a new model, which is based on theoretical expressions for the interfacial-tension, headgroup-steric and chain-conformation components of micelle free energy, along with appropriate expressions for the parameters of the model, including their temperature and curvature dependencies. Special attention was paid to the surfactant chain-conformation free energy, for which a new more general formula was derived. As a result, relatively simple theoretical expressions are obtained. All parameters that enter these expressions are known, which facilitates the theoretical modeling of micelle growth for various nonionic surfactants in excellent agreement with the experiment. The constructed model can serve as a basis that can be further upgraded to obtain quantitative description of micelle growth in more complicated systems, including binary and ternary mixtures of nonionic, ionic and zwitterionic surfactants, which determines the viscosity and stability of various formulations in personal-care and house-hold detergency.
Differential gene expression is not required for facultative sex allocation : A transcriptome analysis of brain tissue in the parasitoid wasp nasonia vitripennis
Cook, Nicola ; Boulton, Rebecca A. ; Green, Jade ; Trivedi, Urmi ; Tauber, Eran ; Pannebakker, Bart A. ; Ritchie, Michael G. ; Shuker, David M. - \ 2018
Royal Society Open Science 5 (2018)2. - ISSN 2054-5703 - 8 p.
Behavioural genetics - Local mate competition - Nasonia - Parasitoid - Sex allocation - Transcriptomics
Whole-transcriptome technologies have been widely used in behavioural genetics to identify genes associated with the performance of a behaviour and provide clues to its mechanistic basis. Here, we consider the genetic basis of sex allocation behaviour in the parasitoid wasp Nasonia vitripennis. Female Nasonia facultatively vary their offspring sex ratio in line with Hamilton’s theory of local mate competition (LMC). A single female or ‘foundress’ laying eggs on a patch will lay just enough sons to fertilize her daughters. As the number of ‘foundresses’ laying eggs on a patch increases (and LMC declines), females produce increasingly male-biased sex ratios. Phenotypic studies have revealed the cues females use to estimate the level of LMC their sons will experience, but our understanding of the genetics underlying sex allocation is limited. Here, we exposed females to three foundress number conditions, i.e. three LMC conditions, and allowed them to oviposit. mRNA was extracted from only the heads of these females to target the brain tissue. The subsequent RNA-seq experiment confirmed that differential gene expression is not
Towards a common conceptual framework and illustrative model for feather pecking in poultry and tail biting in pigs : Connecting science to solutions
Bracke, M.B.M. ; Rodenburg, T.B. ; Vermeer, H.M. ; Niekerk, T.G.C.M. van - \ 2018
Wageningen :
Feather pecking (fp) in poultry and tail biting (tb) in pigs are among the most persistent animal-welfareproblems associated with intensive livestock farming. Both problems have been studied and reviewedextensively (e.g. fp: (Rodenburg et al., 2008; Nicol et al., 2013; Rodenburg et al., 2013); tb: (Schrøder-Petersen and Simonsen, 2001; Bracke et al., 2004a; EFSA, 2007b; Taylor et al., 2010; D’Eath et al., 2014;Valros, 2017)). Legislation and policy initiatives have been discouraging the continued performance ofroutine mutilations (beak treatment and tail docking for fp and tb respectively). However, both poultry andpig farmers generally find it difficult to stop mutilations and prevent and/or treat these injurious behavioursin intensive farming systems. Comparing fp and tb may help address these problems. However, few papershave compared the two forms of abnormal behaviour in detail. One notable exception is the fairly recentOpen-Access publication by Brunberg et al. (2016). These authors discussed similarities and differencesbetween fp and tb, and presented a general model which looks somewhat like an envelope. This publicationis written for a scientific audience, and it is not easy to read for farmers and others interested in solving fp/tbsuch as vets, other farm advisors and NGOs. Also the ‘envelope-shaped’ model presented by Brunberg et al.(2016) is not as appealing as we would (ideally) like it to be. It mainly says that by nature both pigs andpoultry are omnivorous generalists that have (had to) become production specialists via genetic selection andrearing in large-scale intensive systems applying a one-size-fits-all principle. According to Brunberg et al.both the physical and social environment (‘where you are’ and ‘who is with you’), together with animal related factors (‘who you are’) determines ‘what you become’ in terms of fp or tb, i.e. a performer(pecker/biter), victim/receiver or a neutral animal. The authors also hypothesise that the gut-microbiotabrainaxis may play a crucial role which should be investigated further. This is in accordance with thecommon view that fp and tb are multifactorial problems associated with the substantial discrepancy betweenthe natural and the commercial environment resulting in a (seriously) deprived foraging (and/or feeding)motivation that eventually leads to fp/tb (and worse, i.e. cannibalism, if not curtailed adequately). It is not entirely clear, however, why the model (figure) in Brunberg et al. (2016) should look like anenvelope. When looking a bit more closely at the figure, the model appears to encompass everything (theanimal, its history and its entire, physical and social, environment). Only upon more careful examination andin particular when reading the text itself do the further ramifications underlying the model become moreclear. Since we feel the text may be rather inaccessible for practical application in problem solving, oneobjective of these blog posts, therefore, is to compare this model to other models, esp. those developed inour own organisation (Wageningen University & Research), in order to see if we can better highlight theavailable knowledge that should be used to (eventually help) solve the problem in practice. To this end wehave also tried to make the information presented by Brunberg et al. (2016) more accessible, and wesupplemented it with our personal expertise on fp/tb. It is important to emphasise, however, that the primaryaim of this publication is to improve on the available conceptual frameworks to facilitate practicalunderstanding of fp and tb so as to support solving the problem in the future. We do not, however, aim topresent a tool box or cook book for solving fp/tb.
Knowledge gaps and research priorities in the prevention and control of hepatitis E virus infection
Poel, W.H.M. Van der; Dalton, H.R. ; Johne, R. ; Pavio, N. ; Bouwknegt, M. ; Wu, T. ; Cook, N. ; Meng, X.J. - \ 2018
Transboundary and Emerging Diseases 65 (2018)S1. - ISSN 1865-1674 - p. 22 - 29.
Hepatitis E virus - HEV research priorities - Zoonosis
Hepatitis E virus (HEV), family Hepeviridae, is a main cause of epidemic hepatitis in developing countries and sporadic and cluster cases of hepatitis in industrialized countries. There are an increasing number of reported cases in humans especially in industrialized countries, and there is a high potential for transboundary spread of zoonotic genotypes of the virus through the transport of pigs, pig products and by-products. Bloodborne transmission of the virus has been reported with a significant medical concern. To better coordinate HEV research and design better control measures of HEV infections in animals, a group of HEV experts reviewed the current knowledge on the disease and considered the existing disease control tools. It was concluded that there is a lack of in-depth information about the spread of the virus from pigs to humans. The role of animals other than pigs in the zoonotic transmission of the virus to humans and the extent of foodborne transmission are poorly understood. Factors involved in development of clinical disease such as infectious dose, susceptibility and virulence of virus strains need to be studied more extensively. However, such studies are greatly hindered by the absence of a broadly applicable, efficient and sensitive in vitro cell culture system for HEV. Diagnostic tools for HEV are available but need to be further validated, harmonized and standardized. Commercially available HEV vaccines for the control of HEV infection in animal populations are needed as such vaccines can minimize the zoonotic risk for humans. Anti-HEV drugs for treatment of HEV-infected patients need to be studied more extensively. The detailed expert review can be downloaded from the project website at http://www.discontools.eu/.
Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease
Lowe-Power, Tiffany M. ; Hendrich, Connor G. ; Roepenack-Lahaye, Edda von; Li, Bin ; Wu, Dousheng ; Mitra, Raka ; Dalsing, Beth L. ; Ricca, Patrizia ; Naidoo, Jacinth ; Cook, David ; Jancewicz, Amy ; Masson, Patrick ; Thomma, Bart ; Lahaye, Thomas ; Michael, Anthony J. ; Allen, Caitilyn - \ 2018
Environmental Microbiology 20 (2018)4. - ISSN 1462-2912 - p. 1330 - 1349.
Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from healthy plants. Untargeted GC/MS metabolomics identified 22 metabolites enriched in R. solanacearum-infected sap. Eight of these could serve as sole carbon or nitrogen sources for R. solanacearum. Putrescine, a polyamine that is not a sole carbon or nitrogen source for R. solanacearum, was enriched 76-fold to 37 μM in R. solanacearum-infected sap. R. solanacearum synthesized putrescine via a SpeC ornithine decarboxylase. A ΔspeC mutant required≥15 μM exogenous putrescine to grow and could not grow alone in xylem even when plants were treated with putrescine. However, co-inoculation with wildtype rescued ΔspeC growth, indicating R. solanacearum produced and exported putrescine to xylem sap. Intriguingly, treating plants with putrescine before inoculation accelerated wilt symptom development and R. solanacearum growth and systemic spread. Xylem putrescine concentration was unchanged in putrescine-treated plants, so the exogenous putrescine likely accelerated disease indirectly by affecting host physiology. These results indicate that putrescine is a pathogen-produced virulence metabolite.
Ethics of Dietary Guidelines : Nutrients, Processes and Meals
Korthals, Michiel - \ 2017
Journal of Agricultural and Environmental Ethics 30 (2017)3. - ISSN 1187-7863 - p. 413 - 421.
Dietary guidelines - Experts - Food capabilities - Framing - Meals - Nutrients - Power
Dietary guidelines are mostly issued by agrifood departments or agencies of governments, and are the result of power play between interest groups and values. They have considerable influence over food preferences and purchases of consumers. Ethical problems are at stake not only with respect to power strategies and their influence on consumers. In this paper I will consider three different types of guidelines: a nutrient oriented type (like the Dutch or American ones), a process oriented type (Scrinis in Nutritionism: the science and politics of dietary advice, Columbia University Press, New York, 2013) and a meal oriented type (like the Brazilian one). In the nutrient oriented guidelines healthy nutrients and food stuffs are mentioned that excel in containing one or more ‘healthy’ nutrients. Bio- and nutrition scientists and the producers of nutrients, like the sugar, dairy and animal industry, have a lot of influence in this variant. The nutrient oriented framing of food is focussed on individual health. Individuals are implicitly addressed to take responsibility for their own long term health; they have to acquire surveillance and cognitive skills in interpreting their bio data. They don’t need to acquire skills to cook. In the process oriented type, foods and ingredients are categorized according to minimal, refined and reconstituted production processes. Nutrition scientists have the last say here. Consumers do need some food skills to handle fresh products. In the meal oriented guidelines, politicians, social scientists and fresh food producers have prominent responsibilities with respect to the formulation of the guidelines and their application. Buying fresh products, preparing and eating together are the main themes. Food is framed in terms of cooking, and eating and sharing meals. Consumers have to spend time in buying fresh ingredients and cooking; they have to develop food capabilities. The formulation of dietary guidelines is not a neutral operation, but determined by controversies about framings of food and health, responsibilities and also by integrity and self-confidence of experts. It is striking that biological and nutrition scientists often proclaim to possess the final truth on the healthiness of nutrients, and heap scorn on diet gurus. They don’t care that their often incoherent recommendations cause a lot of confusion with consumers and sometimes even lack of trust. I discuss these themes in the paper and will also give some arguments why in the current situation the meal oriented type is ethically more acceptable.
Type I interferon is required for T helper (Th) 2 induction by dendritic cells
Webb, Lauren M. ; Lundie, Rachel J. ; Borger, Jessica G. ; Brown, Sheila L. ; Connor, Lisa M. ; Cartwright, Adam N.R. ; Dougall, Annette M. ; Wilbers, Ruud H.P. ; Cook, Peter C. ; Jackson-Jones, Lucy H. ; Phythian-Adams, Alexander T. ; Johansson, Cecilia ; Davis, Daniel M. ; Dewals, Benjamin G. ; Ronchese, Franca ; Macdonald, Andrew S. - \ 2017
The EMBO Journal 36 (2017)16. - ISSN 0261-4189 - p. 2311 - 2465.
Dendritic cell - Interferon - Priming - Th2
Type 2 inflammation is a defining feature of infection with parasitic worms (helminths), as well as being responsible for widespread suffering in allergies. However, the precise mechanisms involved in T helper (Th) 2 polarization by dendritic cells (DCs) are currently unclear. We have identified a previously unrecognized role for type I IFN (IFN-I) in enabling this process. An IFN-I signature was evident in DCs responding to the helminth Schistosoma mansoni or the allergen house dust mite (HDM). Further, IFN-I signaling was required for optimal DC phenotypic activation in response to helminth antigen (Ag), and efficient migration to, and localization with, T cells in the draining lymph node (dLN). Importantly, DCs generated from Ifnar1-/- mice were incapable of initiating Th2 responses in vivo. These data demonstrate for the first time that the influence of IFN-I is not limited to antiviral or bacterial settings but also has a central role to play in DC initiation of Th2 responses.
Microarray profiling of gene expression in Alpha-Synuclein aggregations and its alteration by natural genetic variation in Caenorhabditis elegans
Wang, Yiru ; Snoek, L.B. ; Sterken, M.G. ; Riksen, J.A.G. ; Cook, D. ; Tanny, R.E. ; Andersen, E.C. ; Kammenga, J.E. ; Harvey, S. - \ 2017
Neurodegenerative diseases (NGDs), such as Alzheimer’s diseases (AD) and Parkinson’s diseases (PD), are characterized by progressive degeneration in the human nervous system. The nematode C. elegans is an excellent model in which to study NGDs due to the high level of conservation of gene functions compared to humans. However, C. elegans research largely relies on a single worm genotype – the canonical N2 strain – limiting the ability to explore how naturally varying alleles alter pathological mechanisms in NGDs. In order to identify how genetic variation acts on NGDs, we analyzed transgenic animals that express aggregating human proteins associated with molecular pathogenic progression of NGDs in five genetic backgrounds.

Here, starting with the original transgenic strain expressing the human synaptic protein alpha-synuclein in an N2 genetic background, we have introgressed the PD transgene (unc-54:: α-Syn:: YFP) into four different wild type genetic backgrounds. Analysis of these new transgenic introgressed lines indicates that transgene effects vary greatly depending on the genetic background. To understand the genetic bases of these phenotypic differences, we have sequenced these new lines to recognize confounder of the heterogeneity in transgenes, measured various aspects of the life history, and investigated gene expression differences by microarray. These analyses identified genes that are up- and down-regulated in all genotypes and genes that expressed at a specific stage to particular genetic backgrounds. For example, the differential developments of those lines have been also confirmed from microarray data that the gene vit-1 expressed at different levels between the lines. Functional enrichment links these genes to the aggregation of alpha-synuclein, which is causative of PD, to the associated developmental arrest, metabolic, and cellular repair mechanisms.

Our studies provide opportunities to observe alterations in traits, including global gene expression, associated with the toxicity of misfolded protein aggregation that could not be readily observed in the canonical N2 background. This is a necessary and important step to identify the alleles responsible for individual variation in the onset and progression of NGDs.

Embodiment and reflexivity : Gaining insight into food lifeways through the chili cook-off in Ajijic, Mexico
Fisher, Eleanor ; Arce, Alberto ; Díaz Copado, F.V. - \ 2017
In: Food, Agriculture and Social Change: The Everyday Vitality of Latin America / Sherwood, Stephen, Arce, Alberto, Paredes, Myriam, Routledge Taylor & Francis Group - ISBN 9781138214972 - p. 21 - 33.
DNA methylation and chromatin architecture contribute to pathogenic fungal genome organization and adaptation
Cook III, D.E. ; Seidl, M.F. ; Kramer, H.M. ; Thomma, B.P.H.J. - \ 2017
In: Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - Genetics Society of America - p. 166 - 167.
Fungal pathogens have evolved diverse strategies to overcome host immunity. During fungal-plant interactions, invading fungi utilize secreted proteins, termed effectors, to avoid or subvert the plant immune response through varied biochemical mechanisms. Effector genes are not randomly distributed across a genome, but often reside in polymorphic regions of the genome, clustering with repetitive DNA. Despite the ubiquity and importance of fungal effectors, our mechanistic understanding of their transcriptional regulation and genome organization remains inadequate. As such, we are addressing two key questions 1) How are in planta effectors transcriptionally regulated? 2) How does repetitive DNA contribute to the evolution of highly variable genomic regions that contribute to fungal virulence? Using a variety of genetic and computational approaches, we are characterizing how DNA modifications and chromatin structure (the organization of DNA in a cell) contribute to the evolution of virulence using the soil-borne fungal pathogen Verticillium dahliae. The genome of V. dahliae is predicted to express numerous homologs of known DNA and chromatin modifying proteins, including three putative DNA methyltransferases. We have identified that a single DNA methyltransferase controls a significant portion of the observed DNA methylation at repetitive DNA. Interestingly, repetitive DNA arising from recent segmental genome duplications are devoid of DNA methylation and are more transcriptionally active relative to repetitive DNA at other loci. Additionally, we are assaying the genome for open chromatin to develop a comprehensive view of how gene regulation and chromatin architecture impacts the evolution of fungal virulence.
Regulation of fungal effector gene expression through chromatin de-condensation
Kramer, H.M. ; Cook III, D.E. ; Seidl, M.F. ; Thomma, B.P.H.J. - \ 2017
In: Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - Genetics Society of America - p. 56 - 56.
Fungal plant pathogens require tight control over the expression of their effector genes which encode secreted proteins that facilitate host invasion. Failure to express such genes at the appropriate time or location during host invasion may lead to interception by the plant host, and thus failure of the infection. In many fungal plant pathogens, effector genes are not randomly distributed over the genome, but localized in distinct genomic regions that are enriched in transposable elements (TEs). TEs can transpose over the genome and thereby affect gene expression or functionality, which may negatively affect the organism. To control TE activity, TE-containing genomic regions are usually structured as heterochromatin, a highly condensed genomic structure that is not accessible to the transcription machinery. Consequently, TEs are generally silenced. Due to the close proximity of many effectors to TEs, they may be held in a co-silenced state. Consequently, upon encountering a host-plant, pathogens will require de-condensation of heterochromatin to appropriately express effector genes. To investigate whether the genomic regions containing effector genes are actively de-condensed during host colonization, we are using chromatin immunoprecipitation (ChIP) to selectively isolate heterochromatic DNA of the broad host-range fungus Verticillium dahliae grown in vitro and in planta. Additionally, we map the genome-wide positioning of nucleosomes to investigate differences between effector genes in TE-rich regions and genes that reside within core regions of the genome. This research will lead to a better understanding of the regulation of effector genes and reveal the importance of chromatin dynamics in this process.
Genome plasticity impacts adaptive genome evolution in the vascular wilt pathogen Verticillium
Seidl, M.F. ; Faino, L. ; Cook III, D.E. ; Kramer, H.M. ; Shi-Kunne, X. ; Berg-Velthuis, G.C.M. van den; Thomma, B.P.H.J. - \ 2017
In: Abstract Book 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - Genetics Society of America - p. 80 - 81.
Genome plasticity enables organisms to adapt to environmental changes and to occupy novel niches. This is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale chromosomal variations, all of which contribute to differences in chromosomal size, organization and gene content. While these mechanisms operate in all organisms, they are particularly relevant for plant pathogens that engage in a co-evolutionary arms race with their hosts. Plant pathogens secrete so-called effectors that contribute to host colonization and counteract host immunity. Effector genes often cluster in highly plastic, transposon-rich genomic regions. However, mechanistic understanding of the evolution of these plastic genomic regions remains scarce. We study these molecular mechanisms in the fungal genus Verticillium that contains economically and ecologically important plant pathogens, among which Verticillium dahliae is the most notorious pathogen that causes vascular wilt disease on >200 plant species. Using long-read sequencing technology, we completely assembled two V. dahliae strains. By comparative genomics, we established that transposable elements play important roles in shaping the genome of V. dahliae. Plastic genomic regions in V. dahliae that contain all known effectors evolve by extensive genomic rearrangements that are mediated by erroneous double-strand breaks, often over transposons. Extensive genomic rearrangements are not only restricted to V. dahliae, but also occur in related Verticillium species. Furthermore, recent segmental duplications are enhanced in the plastic regions. These regions, in contrast to the core genome, are also enriched in active transposons that further contribute to local plasticity. In fungi, transposons are located in tightly condensed chromatin, so called heterochromatin, that is supposed to suppress transposon activity and repress structural variations. In contrast, many fungal pathogens have highly plastic transposon-rich regions. Therefore, research into chromatin opens new avenues to link genome organization, genome plasticity and adaptive genome evolution in fungal pathogens.
The two-speed genome of Verticillium dahliae mediates emergence of potent virulence factors
Thomma, B.P.H.J. ; Faino, L. ; Li, J. ; Shi-Kunne, X. ; Depotter, J.R.L. ; Kramer, H.M. ; Berg-Velthuis, G.C.M. van den; Cook III, David ; Rövenich, H.J. ; Seidl, M.F. - \ 2017
In: Book of Abstracts 29th Fungal Genetics Conference Asilomar 17, Pacific Grove, CA, USA 14-19 March 2017. - - p. 4 - 4.
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, virulence genes reside in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of such compartments, and the role of transposons therein, remains limited. We show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae, and that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. Remarkably, LS regions are enriched in active transposons, which may contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of V. dahliae virulence. Based on this knowledge, we are now able to identify crucial virulence factors of V. dahliae, which also allows investigating causal relationships between particular effectors and pathotypes.
Hard-to-cook phenomenon in bambara groundnut (Vigna subterranea (L.) Verdc.) processing : Options to improve its role in providing food security
Mubaiwa, Juliet ; Fogliano, Vincenzo ; Chidewe, Cathrine ; Linnemann, Anita R. - \ 2017
Food Reviews International 33 (2017)2. - ISSN 8755-9129 - p. 167 - 194.
Bambara groundnut - food security - hard-to-cook phenomenon - hard-to-mill phenomenon - processing - sub-Saharan Africa

Indigenous legume crops are pivotal in providing proteins and food security to sub-Saharan African rural communities, but most of these crops are underutilized because of the so-called hard-to-cook (HTC) phenomenon in combination with inadequate processing techniques. This review studies the case of bambara groundnut, which is third in importance after groundnut and cowpea and especially adapted to semi-arid areas. Published data on the HTC phenomenon implicate microstructural and compositional changes as factors leading to its development. Useful and sustainable techniques to process HTC legumes in developing countries include cooking with alkaline salts, milling, roasting, fermentation, and malting. Improvement of these processing techniques in relation to nutrient bioaccessibility, safety, and consumer acceptance of the products is urgently needed. Recommendations are to lessen the problems of food security in sub-Saharan African countries through, amongst other means, the optimization of bambara groundnut processing methods.

'Children need to relate to their food'
Bouwman, Laura - \ 2016

Youth Food Movement is campaigning this month for compulsory nutritional education in the Netherlands. Children need to learn where food comes from, what a healthy diet is, and how to cook, says the campaigning group. Good idea, says Laura Bouwman, a researcher at the Health and Society chair group.

Youth Food Movement is campaigning this month for compulsory nutritional education in the Netherlands. Children need to learn where food comes from, what a healthy diet is, and how to cook, says the campaigning group. Good idea, says Laura Bouwman, a researcher at the Health and Society chair group.

‘It is important to give children the chance to relate to their food – at home and at school. Seeing, feeling, smelling and tasting food is crucial to then. You could get schoolchildren to grow some food, for instance. If you see how a carrot grows, you’ll be more inclined to eat it. You can get them experimenting with cooking, which makes them start tasting fruit and vegetables. And you can teach them about food in a playful way through puzzles and quizzes. That makes children more willing to try new foods too. They need to be actively involved with it.’

So no lessons about health and overweight?

‘No. At the moment there is too much focus on overeating and wrong dietary choices – in other words, on what is not good. That standard education - scaring children off things - doesn’t work very well because children and adolescents are not very receptive to risk communication. It would be better to tell them what is good, but only once they have experienced it for themselves. You have to challenge children, get them questioning things. That is really necessary because you hear more and more children saying ‘I don’t like vegetables.’ Vegetables haven’t changed but parents and the parties providing them have.

Should schools have a food policy?

‘Schools do have a very clear policy against smoking and alcohol but they don’t usually have a position on healthy food. That kind of policy could help, making a healthy food choice the easiest choice. But even then pupils will go off to the snack bar in the lunch hour and get a hamburger. So you need to challenge your pupils to develop their own point of view on food.’

Chromatin Biology Impacts Adaptive Evolution of Filamentous Plant Pathogens
Seidl, Michael F. ; Cook, David E. ; Thomma, Bart P.H.J. - \ 2016
PLoS Pathogens 12 (2016)11. - ISSN 1553-7366
An organism’s adaptation to changing environments is fueled by its genetic variability, which is established by mechanisms ranging from single-nucleotide polymorphisms to large-scale structural variations, all of which affect chromosomal shape, organization, and gene content [1]. These processes are particularly relevant for pathogens that must respond to continual selection pressure arising from host immune systems that evolved to detect the presence or activity of potentialmicrobial pathogens through a variety of invasion patterns [2]. In their adaptive response, pathogens evolve strategies, often involving secreted effectormolecules, to overcome host immunity and support host colonization [3]. Thus, it can be anticipated that this coevolutionary arms race leads to highly specific interactions between adapted pathogens and their specific hosts. Paradoxically, particular pathogens successfully colonize a broad range of hosts, yet how such pathogens cope in arms races with such a diversity of hosts remains unknown.
Regulating fungal pathogenesis through chromatin modifications
Cook III, D.E. ; Seidl, M.F. ; Kramer, Martin ; Thomma, B.P.H.J. - \ 2016
Plants recognize invading organisms through immune receptors, which must be avoided or subverted to establish a successful symbiosis. A key theme in plant-microbe interactions is that invading organisms utilize effectors, microbially derived molecules, to modulate the plant immune response through varied biochemical processes. Effector expression is tightly regulated and effectors often remain transcriptionally silent outside of specific stages of infection. Despite their importance, mechanistic understanding of how effectors are transcriptionally regulated during growth and infection remains scarce. Recent observations in mainly model fungal systems have begun to link chromatin (the organization of DNA in a cell) to the expression of adaptive genes, but significant questions remain. To address the role of DNA and histone methylation in fungal growth and pathogenesis, we study the soil-borne fungal pathogen Verticillium dahliae. The genome of V. dahliae is predicted to express numerous homologs of chromatin modifying proteins, including three putative DNA methyltransferases. We are using a variety of genetic, proteomic, and computational approaches to characterize the role of DNA and histone modifications in the life history of V. dahliae. We have identified mutants for chromatin modifying proteins that significantly effect fungal growth and plant pathogenesis, including a previously unreported link to DNA methylation. Current data indicate that specific histone modifying proteins negatively regulate effector genes embedded in distinct regions of the genome, and this expression has a strong environmental component. We are studying chromatin dynamics related to gene expression and fungal virulence to elucidate key proteins and pathways regulating these critical proteins.
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