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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    Thank You to Our 2019 Peer Reviewers
    Filippelli, Gabriel ; Colwell, Rita R. ; Anenberg, Susan ; Balbus, John ; Ceccarelli, Daniela ; Hudson-Edwards, Karen A. ; Jutla, Antarpreet ; Miao, Chiyuan ; Sandifer, Paul A. ; Vengosh, Avner - \ 2020
    GeoHealth 4 (2020)3. - ISSN 2471-1403
    editorial - peer review
    Peer review is at the heart of the scientific endeavor, ensuring that high‐quality discoveries are communicated in effective and impactful ways. As a voluntary and mostly anonymous effort, peer review is often poorly recognized. But it is so valuable to journal Editors, and we are often so impressed by the incredibly detailed, constructive, and informative reviews that we get back from reviewers. In 2019, GeoHealth benefited from more than 94 reviews provided by 73 of our peers for papers submitted to the journal. Thank you all for being such an important part of the scientific process, advancing the communication of discoveries at the intersections of the environmental and health sciences to improve society.
    A Global Survey on the Perceptions and Impacts of Gender Inequality in the Earth and Space Sciences
    Popp, Andrea L. ; Lutz, Stefanie R. ; Khatami, Sina ; Emmerik, Tim H.M. van; Knoben, Wouter J.M. - \ 2019
    Earth and Space Science 6 (2019)8. - ISSN 2333-5084 - p. 1460 - 1468.
    gender inequality - leaky pipeline - women in Earth and space science

    The leaky pipeline phenomenon refers to the disproportionate decline of female scientists at higher academic career levels and is a major problem in the natural sciences. Identifying the underlying causes is challenging, and thus, solving the problem remains difficult. To better understand the reasons for the leaky pipeline, we assess the perceptions and impacts of gender bias and imbalance—two major drivers of the leakage—at different academic career levels with an anonymous survey in geoscience academia (n=1,220). The survey results show that both genders view male geoscientists as substantially more gender biased than female scientists. Moreover, female geoscientists are more than twice as likely to experience negative gender bias at their workplaces and scientific organizations compared to male geoscientists. There are also pronounced gender differences regarding (i) the relevance of role models, (ii) family-friendly working conditions, and (iii) the approval of gender quotas for academic positions. Given the male dominance in senior career levels, our results emphasize that those feeling less impacted by the negative consequences of gender bias and imbalance are the ones in position to tackle the problem. We thus call for actions to better address gender biases and to ensure a balanced gender representation at decision-making levels to ultimately retain more women in geoscience academia.

    Bodies of the plant and Animal Kingdom : An illustrated manuscript on materia medica in the Netherlands (ca. 1800)
    Swart, Ingeborg ; Beumer, Mieke ; Klein, Wouter ; Andel, Tinde van - \ 2019
    Journal of Ethnopharmacology 237 (2019). - ISSN 0378-8741 - p. 236 - 244.
    Amsterdam - Animal products - Drug trade - Historical manuscripts - Medicinal plants

    Ethnopharmacological relevance: Around 1800, Amsterdam was a global trade hub for materia medica of Dutch, European and exotic origin. Contemporary knowledge on medicinal plants in academic circles has been well documented in local pharmacopoeia, illustrated herbals and catalogues of botanic gardens. Until the end of the ancient regime, physicians, surgeons and apothecaries were trained how to use plants in their specific guild or Collegium Medicum. Little is known, however, on how the plant collectors and merchants that provided the pharmaceutical substances to apothecaries learnt to recognise the variety of medicinal products. Aim of the study: To analyse the content, origin, purpose and scientific importance of an anonymous, undated, hand-written Dutch manuscript on materia medica, entitled Corpora ex Regno Vegetabili/Animali (Bodies of the Plant/Animal kingdom) kept by the Artis Library of the University of Amsterdam, the Netherlands. Materials and methods: We digitised the entire manuscript and dated the paper by means of its watermark. We identified the plant and animal species using the historic Dutch and Latin names, the illustrations and historic literature. We compared the plant properties and uses to contemporary literature to check whether the information in the manuscript was original or copied from another source. Results: The paper was produced between 1759 and 1816 in Zaandam, the Netherlands. The manuscript contains 19 substances of animal origin, one mineral and 273 plants and plant-derived products, which belong to ca. 260 species. While most plants are native or cultivated in the Netherlands, 111 plant entries (105 spp.) represent exotic products, imported from as far as Madagascar and Australia. A total of 134 illustrations were cut out from a 1549 Dutch edition of the New Herbal by Leonhard Fuchs (1543), but only 69% correspond to the correct species. The manuscript contains detailed descriptions on growth locations, field characteristics, flowering season, provenance and quality of the medicinal products, including methods to detect forgery. The author mostly described humoral properties of the plants rather than listing medicinal recipes. We did not find evidence that he copied his texts from other sources, but the Dutch and Latin names correspond largely with the Amsterdam pharmacopoeia from 1795. Conclusions: The author's extensive knowledge on trade names, quality and origin of materia medica and his refrain from using literature suggests he could have been a merchant, an intermediary between herb cultivators, overseas traders and apothecaries. This manuscript offers a unique insight in the global trade in medicinal products and the circulation of knowledge in non-academic circles around 1800.

    Data from: Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages
    Preite, Veronica ; Oplaat, Carla ; Biere, Arjen ; Kirschner, Jan ; Putten, W.H. van der; Verhoeven, Koen J.F. - \ 2018
    NIOO-KNAW
    DNA methylation - stress memory - drought - salicylic acid - Taraxacum officinale
    DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.
    Water governance as a question of justice : Politics, rights, and representation
    Roth, Dik ; Zwarteveen, Margreet ; Joy, K.J. ; Kulkarni, Seema - \ 2018
    In: Water Justice / Boelens, Rutgerd, Perreault, Tom, Vos, Jeroen, Cambridge University Press - ISBN 9781107179080 - p. 43 - 58.

    Introduction Policy discourses - at the heart of water governance - are seldom explicit about the distributional assumptions and consequences underlying water policies, technologies, and institutions. They treat water problems as natural problems affecting all of us, and proposed solutions are “rendered technical” (Li, 2007) or leave allocation to anonymous markets. This makes it difficult, if not impossible, to recognize that water governance is significantly about justice. Therefore, this chapter shows how making water justice issues visible significantly hinges on defining water governance through water distribution and water rights (see also Zwarteveen, 2015). This starts by acknowledging and teasing out how the socio-environmental processes of change that water interventions (involving institutions, technologies and markets) entail alter existing water stocks, flows, quantity and quality, and create new access patterns and mechanisms, establish new rights and forms of in/exclusion, and thus new constellations of winners and losers (Swyngedouw and Heynen, 2003). Contestation and conflict are intrinsic to such changes, which is why “rational organization of dissent” (see Mollinga, 2008) is essential to water governance approaches that take justice seriously. Debate and disagreement may concern direct physical control over water resources; rules and laws governing water allocation, use and management; authority and power to define, decide upon, and enforce such rules; or the discourses and knowledge used to frame or make sense of society-water relations (Boelens and Zwarteveen, 2005; Zwarteveen et al., 2005).To understand water governance in terms of justice, we recognize that many current water governance reforms are part of broader capitalist transformation under globalization. Dominant water governance language and logic are so deeply infused with neoliberalism that it has become difficult to see and recognize them as part of an ideology or belief rather than a (natural or economic) given or a necessity (see Achterhuis et al., 2010; Ahlers and Zwarteveen, 2009; Boelens and Zwarteveen, 2005). The following section shows how India’s rapid economic growth is partly driven by equally rapid (although neither new nor recent) capitalization of nature, increasingly allocating water resources to supposedly more productive uses - industries and private companies - at the expense of supposedly less-productive users, including smallholder farmers or the urban poor. The state actively supports and facilitates this, reforming water law to standardize and privatize water rights (Cullet et al., 2010a).

    Know your neighbor : The impact of social context on fairness behavior
    Sircar, Neelanjan ; Turley, Ty ; Windt, Peter van der; Voors, Maarten - \ 2018
    PLoS ONE 13 (2018)4. - ISSN 1932-6203
    Laboratory experiments offer an opportunity to isolate human behaviors with a level of precision that is often difficult to obtain using other (survey-based) methods. Yet, experimental tasks are often stripped of any social context, implying that inferences may not directly map to real world contexts. We randomly allocate 632 individuals (grouped randomly into 316 dyads) from small villages in Sierra Leone to four versions of the ultimatum game. In addition to the classic ultimatum game, where both the sender and receiver are anonymous, we reveal the identity of the sender, the receiver or both. This design allows us to explore how fairness behavior is affected by social context in a natural setting where players are drawn from populations that are well-acquainted. We find that average offers increase when the receiver’s identity is revealed, suggesting that anonymous ultimatum games underestimate expected fair offers. This study suggest that researchers wishing to relate laboratory behavior to contexts in which the participants are well-acquainted should consider revealing the identities of the players during game play.
    Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages
    Preite, Veronica ; Oplaat, Carla ; Biere, Arjen ; Kirschner, Jan ; Putten, Wim H. van der; Verhoeven, Koen J.F. - \ 2018
    Ecology and Evolution 8 (2018)5. - ISSN 2045-7758 - p. 3047 - 3059.
    DNA methylation - drought - Europe - salicylic acid - stress memory - Taraxacum officinale
    DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.
    Stakeholders’ perspectives on the operationalisation of the ecosystem service concept: Results from 27 case studies
    Dick, Jan ; Turkelboom, Francis ; Woods, Helen ; Iniesta-Arandia, Irene ; Primmer, Eeva ; Saarela, Sanna-Riikka ; Bezák, Peter ; Mederly, Peter ; Leone, Michael ; Verheyden, Wim ; Kelemen, Eszter ; Hauck, Jennifer ; Andrews, Chris ; Antunes, Paula ; Aszalós, Réka ; Baró, Francesc ; Barton, David N. ; Berry, Pam ; Bugter, Rob ; Carvalho, Laurence ; Czúcz, Bálint ; Dunford, Rob ; Garcia Blanco, Gemma ; Geamănă, Nicoleta ; Giucă, Relu ; Grizzetti, Bruna ; Izakovičová, Zita ; Kertész, Miklós ; Kopperoinen, Leena ; Langemeyer, Johannes ; Montenegro Lapola, David ; Liquete, Camino ; Luque, Sandra ; Martínez Pastur, Guillermo ; Martin-Lopez, Berta ; Mukhopadhyay, Raktima ; Niemela, Jari ; Odee, David ; Peri, Pablo Luis ; Pinho, Patricia ; Patrício-Roberto, Gleiciani Bürger ; Preda, Elena ; Priess, Joerg ; Röckmann, Christine ; Santos, Rui ; Silaghi, Diana ; Smith, Ron ; Vădineanu, Angheluţă ; Wal, Jan Tjalling van der; Arany, Ildikó ; Badea, Ovidiu ; Bela, Györgyi ; Boros, Emil ; Bucur, Magdalena ; Blumentrath, Stefan ; Calvache, Marta ; Carmen, Esther ; Clemente, Pedro ; Fernandes, João ; Ferraz, Diogo ; Fongar, Claudia ; García-Llorente, Marina ; Gómez-Baggethun, Erik ; Gundersen, Vegard ; Haavardsholm, Oscar ; Kalóczkai, Ágnes ; Khalalwe, Thalma ; Kiss, Gabriella ; Köhler, Berit ; Lazányi, Orsolya ; Lellei-Kovács, Eszter ; Lichungu, Rael ; Lindhjem, Henrik ; Magare, Charles ; Mustajoki, Jyri ; Ndege, Charles ; Nowell, Megan ; Nuss Girona, Sergi ; Ochieng, John ; Often, Anders ; Palomo, Ignacio ; Pataki, György ; Reinvang, Rasmus ; Rusch, Graciela ; Saarikoski, Heli ; Smith, Alison ; Soy Massoni, Emma ; Stange, Erik ; Vågnes Traaholt, Nora ; Vári, Ágnes ; Verweij, Peter ; Vikström, Suvi ; Yli-Pelkonen, Vesa ; Zulian, Grazia - \ 2018
    Ecosystem Services 29 (2018)pt. C. - ISSN 2212-0416 - p. 552 - 565.
    The ecosystem service (ES) concept is becoming mainstream in policy and planning, but operational influence on practice is seldom reported. Here, we report the practitioners’ perspectives on the practical implementation of the ES concept in 27 case studies. A standardised anonymous survey (n = 246), was used, focusing on the science-practice interaction process, perceived impact and expected use of the case study assessments. Operationalisation of the concept was shown to achieve a gradual change in practices: 13% of the case studies reported a change in action (e.g. management or policy change), and a further 40% anticipated that a change would result from the work. To a large extent the impact was attributed to a well conducted science-practice interaction process (>70%). The main reported advantages of the concept included: increased concept awareness and communication; enhanced participation and collaboration; production of comprehensive science-based knowledge; and production of spatially referenced knowledge for input to planning (91% indicated they had acquired new knowledge). The limitations were mostly case-specific and centred on methodology, data, and challenges with result implementation. The survey highlighted the crucial role of communication, participation and collaboration across different stakeholders, to implement the ES concept and enhance the democratisation of nature and landscape planning.
    Telers kletsen zich niet zomaar onder de zuiveringsplicht uit
    Anonymous, Anonymus ; Ruijven, J.P.M. van - \ 2017
    Vakblad voor de Bloemisterij 2017 (2017)41. - ISSN 0042-2223 - p. 12 - 13.
    Measuring stress-induced DNA methylation in apomictic Dandelions
    Gurp, Thomas P. van - \ 2017
    Wageningen University. Promotor(en): W.H. van der Putten, co-promotor(en): K.J.F. Verhoeven; A. Biere. - Wageningen : Wageningen University - ISBN 9789463436045 - 176
    taraxacum officinale - epigenetics - dna methylation - inheritance - apomixis - environmental factors - taraxacum officinale - epigenetica - dna-methylering - overerving - apomixis - milieufactoren

    The success or continuous existence of species requires continuous adaptation to changes in the environment to survive and contribute offspring to the next generation. Selection acts on the phenotype, which is in turn determined by the complex interplay of genetic, epigenetic and environmental variation. (Natural) selection leads to ‘survival of the fittest’ or best-adapted individuals to their local environment, ultimately determining which individuals contribute offspring to the next generation. Understanding the mechanisms by which epigenetic and genetic variation can arise and get passed on through generations determines our understanding of inheritance and evolution. Hitherto, the mechanistic understanding of genetics has shaped the scientific view of inheritance and evolution, leading to the gene-centered paradigm of Neo-Darwinism. However, recent studies indicate that besides genetic (DNA sequence) variation, epigenetic variation can also be transmitted between generations. Further studies on the properties and transgenerational dynamics of epigenetic variation are needed to enhance our understanding of heritability and evolution.

    Epigenetic variation has distinct properties and different transgenerational dynamics compared to genetic variation. Epigenetic variation helps to regulate gene expression and determines the different cell types and function in eukaryotes. The main function of DNA methylation, an important part of the epigenetic code, is to prevent the spread of selfish genetic elements in the genome and to establish the different cellular profiles observed in multicellular organisms. One differentiating feature of epigenetic variation compared to genetic variation is that (specific) epigenetic variation can arise under the influence of stress. This can enable a trans-generational stress-response of organisms which can have a positive influence on the phenotype and (natural) selection on either the (enhanced level of) transgenerational phenotypic plasticity or the epigenetic variation itself, potentially influencing natural selection and ultimately evolution. Where genetic variation can be characterized as hard-inheritance, the inheritance of epigenetic variation is often referred to as ‘soft-inheritance’ due to the lower transgenerational stability and resetting that occurs in the intergenerational transfer of epigenetic variation. Epigenetic variation is also often dependent on, or a downstream consequence, of genetic variation, suggesting that it is (in part) determined by genetic variation.

    Mechanistic studies in model species have contributed greatly to the understanding of the molecular mechanisms that control the dynamics of different epigenetic marks present in multicellular organisms. In plants, studies in the model plant Arabidopsis thaliana have resulted in deciphering the most important molecular mechanisms and actors, giving an ever-increasing insight into the dynamics of epigenetic regulation of cells and organisms. A key feature of model systems is the ability to ‘switch’ off certain genes or molecular pathways, for instance via the experimental use of mutants, enabling the study of their role in the heritability of epigenetic marks. DNA methylation is a well-studied epigenetic mark, which has shown high stability even in transgenerational experiments.

    From the perspective of studying epigenetic variation, plants are particularly interesting for several reasons, most importantly: 1) The separation between soma and germline, the Weismann barrier, is less strict in plants compared to other eukaryotes, as in higher plants

    germline cells are formed during floral development from somatic cells (which can occur throughout the life of the plant), whereas in most eukaryotes germline cell development is restricted to a defined point (early) in the organismal development. 2) The sessile nature of plants makes an adaptive plastic response to changing environments an important feature, a plant cannot just walk away when the going gets tough. 3) The transgenerational stability of DNA methylation is higher in plants compared to other eukaryotes such as mammals, in which epigenetic information is erased during germline reprogramming. These factors combined suggest that the potential importance of epigenetic variation in plants might be high.

    In this thesis, I focus on studying DNA methylation in apomictic Dandelions, applying Next Generation Sequencing (NGS) approaches to the study of this non-model plant species. Apomictic dandelions produce seeds that are genetically identical to the ‘mother’ plant, which makes it easier to study the influence of epigenetic variation without confounding effects of genetic variation. Working with Next Generation Sequencing data is still relatively new and therefore not always optimized for specific types of analysis. I discovered a distinct error pattern in RNAseq data that indicated an artificial source of variation that could be traced back to the way the RNAseq libraries were constructed. The first publication of this thesis contains a technical analysis of such artefacts present in RNAseq data, suggesting that these errors are related to random hexamer mispriming during library construction (Chapter 2).

    The main goal of my work is to better understand the role of epigenetic variation in adaptation and plasticity of plants. This role remains poorly understood. This is in part due to the lack of high-resolution techniques that allow for the detailed study of epigenetic marks such as DNA methylation in non-model organisms. Existing techniques for measuring DNA methylation such as methylation sensitive AFLPs offer only information on DNA methylation variation in an anonymous and limited fashion. The plummeting costs of sequencing techniques have enabled large-scale genotyping efforts (focusing on genetic variation only) for a wide variety of non-model organisms. Here, I extended this popular genotyping by sequencing technique, to allow for sequencing-based epigenotyping or epiGBS (chapter 3), which allows for measuring DNA methylation and genetic variation in hundreds of samples simultaneously. I have extensively validated the approach, providing evidence that with the right design, the accuracy of the DNA methylation measurements with epiGBS are as high as those with the gold standard Whole Genome Bisulfite Sequencing.

    An important aim of my PhD research was to investigate the stability of (stress induced) DNA methylation variation in apomictic dandelions and the potential of phenotypic variation underpinned by DNA methylation variation to be subjected to selection. I therefore studied the transgenerational stability of both stress induced and natural DNA methylation variation in different genotypes of apomictic dandelions in a six-generation experiment, comparing DNA methylation patterns between generations and tracking changes in them (chapter 4) using epiGBS. I found clear but limited evidence for environmental induction of heritable DNA methylation changes after application of Jasmonic Acid. Furthermore, I found a significant negative relation between the similarity of DNA methylation patterns and intergenerational distance, indicating epigenetic divergence over generations. I conclude that DNA methylation in both CG and CHG (where H can be any nucleotide except for G) sequence context are heritable and that environmental perturbation can result in heritable DNA methylation changes which are however not widespread.

    A prerequisite for epigenetic variation to contribute to adaptation is that epigenetic variants that affect the phenotype are heritable. To test whether an epigenetics-based selection response is possible, at least over the time course of a few generations, I selected early flowering for two subsequent generations in three genotypes of apomictic dandelions. This selection effort included lines that received a stress pre-treatment with either Jasmonic Acid or 5-azacytidine, to determine if stress-induced DNA methylation variation would increase the capacity to respond to selection. The selection experiment on flowering time (chapter 5) resulted in a shift in flowering time for all treatments in a young apomict, suggesting that natural and heritable epigenetic variation can underpin quantitative traits such as flowering time. I also found evidence for treatment induced (epi)genetic variation leading to a stronger selection response in one out of 3 genotypes. This suggests that stress- induced heritable epigenetic variation can lead to a selection response. Further study is however required to rule out genetic variants and to study the long-term stability of the variation selected upon.

    Finally, in the General Discussion I summarize the findings, putting them in context with recently published studies. I reflect on the state of the field of ecological epigenetics and in what sense the epiGBS technique that I developed and other emerging techniques can contribute to a better understanding of the role of epigenetic variation in ecology and evolution. I reflect on the place of epiGBS compared to other techniques. I point out that with the growing evidence of the inadequacy and misinterpretation of MS-AFLP results a systematic review of such results by replicating the studies employing sequencing based techniques such as epiGBS instead of MS-AFLP is in order.

    From personalized exchange towards anonymous trade: A field experiment on the workings of the invisible hand
    Bulte, Erwin ; Kontoleon, Andreas ; List, John ; Turley, Ty ; Voors, Maarten - \ 2017
    Journal of Economic Behavior and Organization 133 (2017). - ISSN 0167-2681 - p. 313 - 330.
    Africa - Anonymity - Efficiency - Social relations - Status - Trade experiment
    The experimental literature has shown the tendency for experimental trading markets to converge to neoclassical predictions. Yet, the extent to which theory explains the equilibrating forces in markets remains under-researched, especially in the developing world. We set up a laboratory in 94 villages in rural Sierra Leone to mimic a real market. We implement several treatments, varying trading partners and the anonymity of trading. We find that when trading with co-villagers average efficiency is somewhat lower than predicted by theory (and observed in different contexts), and markets do not fully converge to theoretical predictions across rounds of trading. When participants trade with strangers efficiency is reduced more. Anonymizing trade within the village does not affect efficiency. This points to the importance of behavioral norms for trade. Intra-village social relationships or hierarchies, instead, appear less important as determinants of trading outcomes. This is confirmed by analysis of the trader-level data, showing that individual earnings in the experiment do not vary with one's status or position in local networks.
    Psychosocial factors influencing preferences for food and nutritional supplements among people living with HIV in Bangkok, Thailand
    Rodas Moya, Carlos ; Pengnonyang, Supabhorn ; Kodish, Stephen ; Pee, Saskia de; Phanuphak, Praphan - \ 2017
    Appetite 108 (2017). - ISSN 0195-6663 - p. 498 - 505.
    Food preferences - HIV - Nutritional supplements - Psychosocial factors

    Malnutrition and HIV are often coincident and may lead to wasting, a strong predictor of mortality. However; ready to use therapeutic foods (RUTF) are showing promising results in restoring the nutritional status of adult people living with HIV (PLHIV) in resource constrained settings but, its acceptability seems low. This study aimed to identify the psychosocial factors influencing general preferences for food and responses to five potential nutritional supplements to guide the development of novel products to treat malnutrition among PLHIV. This is a qualitative research based on Grounded Theory. In-depth interviews (IDIs) with a triangulation of data from different participants (i.e. PLHIV and Peer Counselors (PCs) were used as methods for data collection. During February-March 2013, 27 IDIs were conducted in the Anonymous Clinic of the Thai Red Cross and AIDS Research Center in Bangkok, Thailand. Five themes emerged: 1) local food culture is an important motive underlying the nutritional supplements choice by PLHIV; 2) food and drinks should have self-perceptible positive impact on health status and should be perceived convenient; 3) a soft and easy to swallow texture, softer scents and flavors are the major sensory characteristics guiding food and beverages choice; 4) food packaging characteristics affect nutritional supplement preference; 5) PCs may support nutritional supplement consumption. Similar findings emerged among PLHIV and PCs. This study highlights the need to develop a nutritional supplement considering the Thai culture and PLHIV's sensory preferences. A slightly thick liquid supplement, packed in small containers may be well-accepted. A combination of sensory studies and formative research should accompany the development of an alternative nutritional supplement for PLHIV. Results of this study might be transferable to similar sociocultural contexts.

    Onderzoek mogelijkheden uitbreiding uitzonderingslijst Producten v.w.b. vermelding houdbaarheidsdatum/THT
    Anonymous, - \ 2015
    Wageningen : RIKILT - 10
    Attitude toward living kidney donation : Differences between students from two spanish universities
    Martínez-Alarcón, L. ; Ramis, G. ; Gómez-Laguna, J. ; Quereda, J.J. ; Herrero-Medrano, J.M. ; Mrowiec, A. ; Mendonça, L. ; López-Navas, A. ; Ríos, A. - \ 2015
    Transplantation Proceedings 47 (2015)1. - ISSN 0041-1345 - p. 10 - 12.

    Introduction Due to the current deficit of organs for transplantation, living kidney related donations (LKRD) should be promoted. Veterinarians often hold decision-making positions in the public health care system, and therefore can influence public opinion about organ donation. The objective was to analyze the attitude of Spanish veterinary students toward LKRD because they may influence public opinion in the future, and to determine the factors that condition it. Materials and Methods The study was carried out among fifth-year veterinary science students from 2 southern and southeastern Spanish universities. The students' attitude toward LKRD was assessed using a psychosocial, anonymous, self-administered questionnaire. Statistics used were χ2 test and Student t test. Results Data from the southern Spain university included a response rate of 87%. The survey showed that 94% of respondents would donate a kidney to a relative who needed it. This attitude toward LKRD was more favorable in women (P

    GLAMUR case-study report: The comparison of three Dutch pork cases (Tasks 3.5)
    Oostindië, H.A. ; Horlings, L.G. ; Broekhuizen, R.E. van; Hees, E. - \ 2015
    Wageningen : Wageningen UR - 72
    pig farming - case studies - netherlands - supply chain management - performance - animal production - intensive livestock farming - sustainable animal husbandry - regional food chains - animal welfare - pigs - animal housing - varkenshouderij - gevalsanalyse - nederland - ketenmanagement - prestatieniveau - dierlijke productie - intensieve veehouderij - duurzame veehouderij - regionale voedselketens - dierenwelzijn - varkens - huisvesting, dieren
    This report presents the case study results of local-global pork chain performances in The Netherlands. As part of Work Package 3, this case study was carried out in cooperation with our Italian GLAMUR partner. The Dutch pork production sector came up after World War 2 and developed into a highly intensified and specialized sector, with emphasis in the southern part of the country. As it became possible and economically attractive to transport fodder ingredients over great distances, pig husbandry became a booming sector, with high technology and knowledge input, and a major exporting sector. In the last decade, the number of pig farms reduced sharply, whereas the number of pigs per farm rose constantly. As a consequence of a combination of factors as pig disease outbreaks in the late 90-s, environmental externalities, growing national opposition against animal welfare conditions ánd growing international competition, the pig sector came to a standstill. In this study three chains are compared: first the Good Farming Global pork chain, to be considered Dutch most typical bulk pork chain, oriented towards more anonymous far-from-home markets with basic requirements in terms of low-priced, food safe and mainstream qualified. The second is the Sustainable Pork Chain, developed some 10 years ago on the Environmental certification schema (MK) as a transparent pork chain towards specialized butchers and more critical retailers. Third, the so-called Lupine Pig project has been analyzed, an early-life cycle initiative that responds to national growing demand for more locally sourced pork production.
    Restyling Alternaria
    Woudenberg, J.H.C. - \ 2015
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit, co-promotor(en): J.Z. Groenewald. - Wageningen : Wageningen University - ISBN 9789462574106 - 250
    alternaria - taxonomie - fylogenie - moleculaire taxonomie - plantenziekteverwekkende schimmels - alternaria - taxonomy - phylogeny - molecular taxonomy - plant pathogenic fungi

    The omnipresent dematiaceous hyphomycete genus Alternaria is associated with a wide variety of substrates including seeds, plants, agricultural products, humans, soil and even the atmosphere. It includes saprophytic, endophytic and pathogenic species, among which multiple plant pathogens, post-harvest pathogens, and human pathogens (causative agents of phaeohyphomycosis and hypersensitivity reactions). Molecular studies reveal that the Alternaria complex comprises nine genera. Within this complex several genera are non-monophyletic and Alternaria species cluster into multiple distinct species clades, which are not always correlated with species-groups based on morphological characteristics. The most commonly reported species in literature and type species of the genus Alternaria, A. alternata, also comprises one such species-group. The small-spored Alternaria species within this group are mainly described based on morphology and / or host-specificity, but are difficult to distinguish based on molecular techniques alone. As A. alternata is considered as one of the most prolific producers of fungal allergens and is reported as pathogen on over 100 host plants, correct species identification is of utmost importance. The research presented in this thesis discusses the taxonomic status of Alternaria and its related genera, with a further focus on the two biggest and most important species complexes; the large-spored A. porri and small-spored A. alternata species complexes. With the phylogenies and classifications presented in this thesis, more robust and understandable taxonomy and nomenclature in Alternaria and allied genera within the Alternaria complex are created.

    Chapter 1 gives a general introduction to the genus Alternaria and related genera. The history of the genus and its economic importance as plant pathogen, post-harvest pathogen, causative agent of phaeohyphomycosis and common allergen causing hypersensitivity reactions are summarized. The introduction of the morphological species complexes, based on characters of the conidia, the pattern of chain formation, and the nature of the apical extensions of conidia are treated. Molecular studies recognise seven Alternaria species-groups within the Alternaria complex. Besides Alternaria, eight other genera are assigned to the Alternaria complex based on molecular and morphological studies.

    Chapter 2 focusses on the relationship of Alternaria and its closely related genera within the broader Alternaria complex. The phylogenetic lineages within the Alternaria complex are delineated based on nucleotide sequence data of parts of the 18S nrDNA (SSU), 28S nrDNA (LSU), the internal transcribed spacer regions 1 and 2 and intervening 5.8S nrDNA (ITS), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF1) gene regions. The phylogenetic data reveal a Stemphylium clade sister to Embellisia annulata and a big Alternaria clade. The Alternaria clade contains six monotypic lineages and 24 internal clades, which are treated as sections of Alternaria. In order to create a stable phylogenetic taxonomy, and supported by i) a well-supported phylogenetic node in multiple analyses, ii) a high-similarity of clades within Alternaria based on SSU, LSU and ITS data, and iii) variation in the clade order between the different gene phylogenies, 13 genera are placed into synonymy with Alternaria. Embellisia annulata is synonymized with Dendryphiella salina, and together with D. arenariae placed in the new genus Paradendryphiella. The sexual genera Clathrospora and Comoclathris, with asexual forms linked to Alternaria, cluster within the Pleosporaceae, as does Alternaria, but outside Alternaria s. str. The genus Alternariaster, described to accommodate Alternaria helianthi, clusters within the Leptosphaeriaceae.

    Chapter 3 describes the reappraisal of the genus Alternariaster. Alternaria helianthi, the causal agent of leaf spot on Helianthus annuus (sunflower) was segregated from Alternaria based on conidial morphology, and placed in the new genus Alternariaster. A multi-gene phylogeny of parts of the ITS, LSU, RPB2 and GAPDH gene regions placed a fungal pathogen associated with leaf spot on Bidens sulphurea (yellow cosmos) in Brazil in close relation with Al. helianthi. Based on the close phylogenetic relation to Al. helianthi, but distinct morphological and pathogenicity characters, the fungal pathogen associated with leaf spot on B. sulphurea is newly described as Al. bidentis.

    Chapter 4 treats the Alternaria species which form the largest section of Alternaria, sect. Porri. This section contains almost all Alternaria species with medium to large conidia with long beaks, some of which are important plant pathogens. A multi-gene phylogeny on parts of the ITS, GAPDH, RPB2, TEF1 and Alternaria major allergen (Alt a 1) gene regions, supplemented with morphological and cultural studies, forms the basis for species recognition in this section. The polyphasic data reveal 63 species in sect. Porri, of which 10 are newly described, and 27 names are synonymized.

    Chapter 5 treats the small-spored Alternaria species, which reside in sect. Alternaria. A lot of confusion around the naming of species within this section exists, since the naming is mostly based on morphology and host-specificity, although the molecular variation is minimal. Whole genome sequencing, combined with transcriptome profiling and multi-gene sequencing of nine gene regions, SSU, LSU, ITS, GAPDH, RPB2, TEF1, Alt a 1, endopolygalacturonase (endoPG) and an anonymous gene region (OPA10-2), is used to create a clear and stable species classification in this section. The nine sequenced Alternaria genomes range in size from 32.0 - 39.1 Mb. The number of repetitive sequences varies significantly, with a relative low percentage of repeats within sect. Alternaria. The genome identity within sect. Alternaria is high, compared to the genome identity for isolates from other sections to the A. alternata reference genome. Similarly, a relative low percentage of single nucleotide polymorphisms (SNPs) were observed in genomic and transcriptomic sequences between isolates from sect. Alternaria, compared to the percentage of SNP’s found in isolates from different sections compared to the A. alternata reference genome. A set of core proteins was extracted from the genome and transcriptome data, and primers were designed on two eukaryotic orthologous group (KOG) protein loci with a relatively low degree of conservation within section Alternaria. The phylogenies from these two gene regions, KOG1058 and KOG1077, could not distinguish the described morphospecies within sect. Alternaria better than the phylogenies based on the nine commonly used gene regions for Alternaria. Based on genome and transcriptome comparisons and molecular phylogenies, Alternaria sect. Alternaria consists of only 11 phylogenetic species and one species complex. Thirty-five morphospecies are synonymized under A. alternata. The subclades that are formed by these isolates are incongruent between the different gene regions sequenced; no two genes show the same groupings for any of the over 100 isolates. A sequence-based identification guide is provided for the species which are now recognized in sect. Alternaria. None of the genes sequenced in this study can distinguish all of the species recognized here on its own.

    Chapter 6 investigates the molecular diversity of indoor Alternaria isolates in the USA, with the help of a phylogeographic / population genetic approach. Isolates collected throughout the USA were identified using ITS, GAPDH and endoPG gene sequencing, followed by genotyping and population genetic inference of the sect. Alternaria isolates and 37 reference isolates, using five microsatellite markers. Phylogenetic analyses revealed that 98 % (153 isolates) of the indoor isolates consisted of species from Alternaria sect. Alternaria. The remaining 2 % (three isolates) represented one sect. Infectoriae and two sect. Pseudoulocladium isolates. From the 153 isolates that belonged to sect. Alternaria, one could be assigned to A. burnsii, 15 to the A. arborescens species complex and the remaining 137 isolates were identified as A. alternata. Based on the microsatellite data, no specific indoor population could be distinguished. Population assignment analyses of the A. alternata isolates suggested that subpopulations did not exist within the sample, which we thus divided into four artificial subpopulations to represent four quadrants of the USA. Genotypic diversity was extremely high for all quadrants and a test for linkage disequilibrium suggested that A. alternata has a cryptic sexual cycle. The SouthWest-USA population displayed the highest level of uniqueness, based on private alleles. Intriguingly, the highest amount of gene flow, between SouthWest-USA and SouthEast-USA, correlated with the west-to-east movement of the antitrade winds. This suggests that indoor A. alternata isolates, although extremely diverse, have a continental distribution and high levels of gene flow over the continent.

    Chapter 7 discusses the data presented in this thesis. The implications of the performed studies are placed in a broader context, with a focus on the relation between morphology and the new species classification based on molecular tools and the use of genome data in contrast to multi-gene data.

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