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.

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Measuring stress-induced DNA methylation in apomictic Dandelions
Gurp, Thomas P. van - \ 2017
University. Promotor(en): Wim van der Putten, co-promotor(en): K.J.F. Verhoeven. - Wageningen : Wageningen University - ISBN 9789463436045 - 176
taraxacum officinale - epigenetics - dna methylation - inheritance - apomixis - environmental factors - epigenetica - dna-methylering - overerving - 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.

Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis
Morales Sierra, Alejandro - \ 2017
University. Promotor(en): Paul Struik; Jaap Molenaar, co-promotor(en): Xinyou Yin; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789463430456 - 282
photosynthesis - modeling - analysis - environmental factors - light - canopy - leaves - crop physiology - metabolism - fotosynthese - modelleren - analyse - milieufactoren - licht - kroondak - bladeren - gewasfysiologie - metabolisme

In their natural environment, leaves are exposed to rapid fluctuations of irradiance. Research on CO2 assimilation under fluctuating irradiance often relies on measurements of gas exchange during transients where irradiance is rapidly increased or decreased, after the leaf has adapted to a particular set of environmental conditions. In the field, such increases and decreases occur mostly because of sunflecks (rapid increases in irradiance on a low irradiance background) created by gaps in the canopy and plant movement by wind, and cloudflecks (rapid decreases in irradiance on a high irradiance background) generated by clouds that transiently block the sun.

In this dissertation, the metabolic regulation of photosynthesis and how this may limit dynamic CO2 assimilation is studied in silico with the development and application of simulation models. In order to support the development of the models, a review of the literature was performed as well as an experiment designed to generate data on dynamic CO2 assimilation for different photosynthetic mutants of Arabidopsis thaliana. In addition to providing these models to the research community, this dissertation also identifies multiple targets that may be used for improving dynamic CO2 assimilation in plants. It further demonstrates that the dynamic responses of CO2 assimilation to changes in irradiance has a significant effect on canopy CO2 assimilation, even for dense canopies exposed to open skies, resembling the conditions of commercial crops.

In Chapter 1, the context of this dissertation is presented. The societal relevance of this research is argued, making reference to the role that photosynthesis could play in addressing global problems such as food and energy security. The necessary background on the physiology of photosynthesis is provided, with special emphasis on the terminology and concepts required to understand the rest of the dissertation, with the aim of making the contents more accessible to a wider audience. Then, prior literature on the specific topics of this dissertation (i.e., photosynthesis in a dynamic environment and its mathematical modelling) is presented, with a chronological approach that analyses the evolution of ideas and methodologies up to the present.

In Chapter 2, the current literature on dynamic CO2 assimilation is reviewed, with an emphasis on the effects of environmental conditions ([CO2], temperature, and air humidity) on the rates of photosynthetic induction and loss of induction. This review reveals major knowledge gaps, especially on the loss of induction. The little data available indicates that rates of photosynthetic induction increase with [CO2], which could be explained by a weak effect on Rubisco activation and a strong effect on stomatal opening. Increases in temperature also increase the rates of photosynthetic induction, up to an optimum, beyond which a strong negative effect can be observed, which could be attributed to deactivation of Rubisco activase.

In Chapter 3, an experiment is presented that makes use of several photosynthetic mutants of A. thaliana. Downregulating non-photochemical quenching and sucrose synthesis did not have any significant effect on dynamic CO2 assimilation, whereas CO2 diffusion and Rubisco activation exerted stronger limitations. Further analysis reveals that whether stomatal opening limits CO2 assimilation after an increase in irradiance depends on the stomatal conductance prior to the change in irradiance. A threshold value of 0.12 mol m−2 s−1 (defined for fluxes of water vapour) could be defined, above which stomata did not affect the rates of photosynthetic induction. The comparison of measurements across irradiance levels also indicated that the apparent rate constant of Rubisco activation is irradiance-dependent, at least for irradiance levels below 150 μmol m−2 s−1.

In Chapter 4, a phenomenological model of leaf-level CO2 assimilation is presented. The model is described in detail and all the parameters are first estimated with published data, and later refined by fitting the model to the data from Chapter 3. Additional data from the experiment in Chapter 3 is used to validate predictions of CO2 assimilation under lightflecks for the different photosynthetic mutants. The model predicts accurately dynamic CO2 assimilation for the different photosynthetic mutants by only modifying those parameters that are affected by the mutation. This demonstrates that the model has a high predictive power and that the equations, although phenomenological in nature, have a solid physiological basis.

The model is further used to analyse, in silico, the limitations imposed by different photosynthetic processes on dynamic CO2 assimilation at the leaf and canopy level, allowing a more in depth analysis than in Chapter 3. The analysis demonstrates that results obtained at the leaf level should not be extrapolated directly to the canopy level, as the spatial and temporal distribution of irradiance within a canopy is more complex than what is achieved in experimental protocols. Both at the leaf and canopy level, CO2 diffusion is strongly limiting, followed by photoinhibition, chloroplast movements and Rubisco activation.

In Chapter 5, a mechanistic model of the dynamic, metabolic regulation of the electron transport chain is presented. The model is described in detail and all the parameters are estimated from published literature, using measurements on A. thaliana when available. Predictions of the model are tested with steady-state and dynamic measurements of gas exchange, chlorophyll fluorescence and absorbance spectroscopy on A. thaliana, with success.

The analysis in silico indicates that a significant amount of alternative electron transport is required to couple ATP and NADPH production and demand, and most of it is associated with nitrogen assimilation and export of redox power through the malate shuttle. The analysis also reveals that the relationship between ATP synthesis and the proton motive force is highly regulated by the concentrations of substrates (ADP, ATP and inorganic phosphate), and this regulation facilitates an increase in non-photochemical quenching under conditions of low metabolic activity in the stroma.

In Chapter 6, the findings of Chapters 2–5 are summarised and employed to answer in detail the four research questions formulated in Chapter 1. Of great interest is the identification of six potential targets that may be used to improve dynamic CO2 assimilation. These targets are: (i) regulation of Rubisco activity through changes in the amount or regulation of Rubisco activase, (ii) acceleration of stomatal opening and closure, (iii) a lower /ATP for ATP synthesis, (iv) faster relaxation of non-photochemical quenching, (v) reduced chloroplast movements, and (vi) reduced photoinhibition by increased rates of repair of Photosystem II.

Plant reageert bij bloei op externe signalen als temperatuur en daglengte : vernalisatie zorgt voor het juiste bloeitijdstip
Heuvelink, E. ; Kierkels, T. - \ 2016
Onder Glas 13 (2016)12. - p. 40 - 41.
temperatuur - fotoperiode - planten - bloei - milieufactoren - temperature - photoperiod - plants - flowering - environmental factors
Een plant die op het punt staat te gaan bloeien, kan zich niet bedenken als de omstandigheden toch tegen blijken te vallen. De overgang naar de bloei is onomkeerbaar. Daarom is het van het grootste belang voor het voortbestaan van de soort dat de bloei precies op het juiste tijdstip valt. Om dat voor elkaar te krijgen, reageert de plant op externe signalen, vooral de temperatuur en de daglengte.
Groene daken in Tilburg : ervaringen, motieven en opschalingsmogelijkheden
Hendriks, Kees ; Hommes, Saskia - \ 2016
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2767) - 49
groene daken - groene gevels - beplantingen - warmtestress - stedelijke gebieden - welzijn - luchtkwaliteit - temperatuur - regenwateropvang - milieufactoren - openbaar groen - green roofs - green walls - plantations - heat stress - urban areas - well-being - air quality - temperature - water harvesting - environmental factors - public green areas
Green roofs can contribute to climate adaptation and a sustainable urban environment. Whether
municipalities for these or other reasons should encourage green roofs, depends on the goals that are
aimed at. For the municipality of Tilburg opportunities were investigated for usage of green roofs as
measure for climate adaptation and for scaling up green roof in Tilburg and other municipalities. In
three projects in Tilburg the opportunities for the application of green roofs and the attitude of actors
involved were investigated. Also, the experiences of six other municipalities, which are promoting
green roofs, were examined. The type of project, purpose, and insight in costs and benefits affect the
attitude of actors and hence the opportunities for application and scaling. In the examined
municipalities green roofs in general are stimulated with subsidy, communication and pilot projects.
The experience with green roofs in other municipalities are predominantly positive.
Afstand tussen veehouderij en woningen : een onderzoek naar aantallen veehouderijen en woningen op minder dan 250 meter van elkaar
Os, J. van; Smidt, R.A. ; Jeurissen, L.J.J. - \ 2016
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2658) - 51
veehouderij - landbouwbedrijven - woningen - milieu - milieufactoren - nederland - livestock farming - farms - dwellings - environment - environmental factors - netherlands
Ter voorbereiding op een debat in de Tweede Kamer op 15 september 2014 heeft het ministerie van Economische Zaken aan Alterra gevraagd om te bepalen hoeveel veehouderijen er liggen op een afstand van 250 m of minder van burgerwoningen, niet zijnde agrarische bedrijfswoningen. Achtergrond van deze vraag is de mogelijke negatieve beïnvloeding van de omgevingskwaliteit van woningen door veehouderijen. Naar aanleiding van het debat en het eerste gepubliceerde document heeft het ministerie van Economische Zaken Alterra gevraagd om een actualisatie en nadere detaillering te maken van de eerste resultaten. Met behulp van GIS heeft Alterra daarop zowel voor de jaren 2011 en 2013 bepaald dat ca. 70-90% van de veehouderijen op minder dan 250 m van een woning ligt. Andersom geredeneerd ligt ca. 30-40% van de woningen in het buitengebied op minder dan 250 m van een veehouderij; voor woningen in bevolkingskernen is dat 3%. Binnen Nederland zijn er aanzienlijke verschillen tussen regio’s, vooral veroorzaakt door verschillen in dichtheid van veehouderijen en woningen.
Characterisation of Lactobacillus plantarum single and multi-strain biofilms
Fernández Ramírez, Mónica D. - \ 2016
University. Promotor(en): Tjakko Abee; Eddy Smid, co-promotor(en): Masja Nierop Groot. - Wageningen : Wageningen University - ISBN 9789462579217 - 169
lactobacillus plantarum - biofilms - food spoilage - models - environmental factors - voedselbederf - modellen - milieufactoren

Biofilms consist of microorganisms attached to a surface and embedded in a protective matrix of extracellular polymeric substances. Within a biofilm, micro-organisms are protected from harsh environmental conditions including those resulting from cleaning and disinfecting agents leading to food safety and quality issues after dispersal of life biofilm cells and subsequent contamination of foods. In this thesis, single and multi-strain biofilm formation by Lactobacillus plantarum isolates was characterised including the model strain L. plantarum WCFS1 and food spoilage isolates. Analysis of the L. plantarum single strain biofilm formation showed a role for proteins and/or proteinaceous material in surface colonization and extracellular DNA as components of the biofilm matrix. The relevance of lysis for the build-up of the biofilm matrix with eDNA was demonstrated using L. plantarum WCFS1 mutants affected in the production of cell wall polysaccharides resulting in altered cell surface composition and mutants lacking cell wall lytic enzymes that showed decreased cell lysis. Dual and multi-strain biofilms were studied using quantitative PCR and next generation sequencing based on detection of strain specific alleles in competitive planktonic and surface-attached biofilm growth models. In multi-strain cultures, the performance of individual strains generally correlated with their performance in pure culture, and relative strain abundance in multi-strain static biofilms positively correlated with the relative strain abundance in suspended (planktonic) cultures. Performance of individual strains in dual-strain biofilms was highly influenced by the presence of the secondary strain, and in most cases no correlation between the relative contributions of viable planktonic cells and viable cells in the biofilm was noted. The next generation sequencing approach provided additional insights in the performance of twelve individual L. plantarum strains in static and dynamic flow competitive biofilm models and showed that environmental stresses such as absence of Mn(II) and increased temperature affected not only the relative abundance of each strain both in planktonic and static biofilm growth but also the release of eDNA. The strains dominating the biofilms in static conditions were not the same as those dominating in biofilms developed in dynamic flowing conditions. The genome content of the dominating strains was explored to identify genetic factors that potentially contribute to strain specific competitive-biofilm forming capacity under dynamic flowing conditions, providing leads for further research. All the single, dual and multi-strain biofilms contained a considerable number of viable L. plantarum cells, representing a potential source of contamination. The developed tools and insights obtained in L. plantarum biofilm formation capacity may assist development of strategies to prevent (re)contamination from biofilms in food processing environments.

Berg Roses tests smart horizontal fans : 'In the greenhouse temperature differences not easy to solve'
Weel, Peter van - \ 2016
horticulture - greenhouse horticulture - greenhouse technology - air conditioning - temperature - rosaceae - environmental factors - artificial ventilation

Last year Berg Roses trialles the Verti-Fan in combination wirh two screens that permanently had a gap. The gap and the wind had a far greater inmpact than the fans. This year they are starting a trial with vertical fans that can suck air from above a closed screen, and if necescary mix with greenhouse air. "Air movement in a large greenhouse is like a tanker at sea. It can't be stopped" Thats how Peter van Weel of Wageningen UR Greenhouse described the problem.

Omgevings- en gewasconditie essentieel bij bestrijding meeldauw : Telers wachten met smart op effectieve beheerstrategieën.
Hofland-Zijlstra, Jantineke - \ 2016
horticulture - greenhouse horticulture - cut flowers - pot plants - vegetables - gerbera - tomatoes - kalanchoe - fungal diseases - mildews - environmental factors - defence mechanisms

geJantineke hofland bij de jonge gerberaplanten in een klimaatkast: "In de startblokken voor een nieuwe proef met meeldauw"

Milieufactoren en beschikbaarheid nectar en stuifmeel in graslanden
Ozinga, W.A. ; Geerts, R.H.E.M. ; Hennekens, S.M. ; Schaminee, J.H.J. - \ 2016
Landschap : tijdschrift voor Landschapsecologie en Milieukunde 33 (2016)1. - ISSN 0169-6300 - p. 45 - 47.
functionele biodiversiteit - graslanden - milieufactoren - nectar - stuifmeel - ecosysteemdiensten - bloemen - plantengemeenschappen - functional biodiversity - grasslands - environmental factors - pollen - ecosystem services - flowers - plant communities
Plantengemeenschappen spelen bij veel ecosysteemfuncties en -diensten een cruciale rol. De bijdrage van plantensoorten hangt af van functionele eigenschappen als het aanbod van nectar en stuifmeel in bloemen. Lokale plantengemeenschappen verschillen sterk in het spectrum aan eigenschappen van de soorten en inzicht in deze variatie kan helpen bij duurzaam beheer en gebruik van deze functionele diversiteit. Stilgestaan wordt bij factoren die de variatie in het aanbod van nectar en stuifmeel in graslanden beïnvloeden.
Rapport Honingbijen : Surveillance Programma 2014
Biesmeijer, K. ; Groot, G.A. de; Rijk, T.C. de; Steen, J.J.M. van der - \ 2015
Leiden : Naturalis Biodiversity Center - 16 p.
apidae - honingbijen - bijenhouderij - diergezondheid - bijenziekten - bijensterfte - varroa - overheidsbeleid - landbouwkundig onderzoek - nederland - pesticiden - milieufactoren - honey bees - beekeeping - animal health - bee diseases - bee mortality - government policy - agricultural research - netherlands - pesticides - environmental factors
Naar aanleiding van het door staatssecretaris Sharon Dijksma geïnitieerde brede-maatschappelijke overleg over de gezondheid van bijen zijn verschillende partijen in actie gekomen en is er een gezamenlijke agenda vastgesteld. Topprioriteit kreeg het vaststellen van de oorzaken voor de sterfte van honingbijenvolken in Nederland. Het ministerie van Economische Zaken (EZ) heeft vervolgens opdracht gegeven aan een consortium onder leiding van Prof. Dr. Koos Biesmeijer van Naturalis Biodiversity Center en de Universiteit van Amsterdam om dit consortium te leiden en vorm te geven. De hoofdfinancier is EZ (51%) met Nefyto als co-financier (49%), het totale budget bedraagt maximaal 1.2 miljoen euro en het project zal lopen van 2014 tot 2018. Hoofddoel: Vaststellen van de status van de gezondheid van honingbijen in Nederland en het in kaart brengen van de risicofactoren die correleren met de wintersterfte van volken, waaronder blootstelling aan gewasbeschermings-middelen, bijenziekten, voedselaanbod, landschap en milieu, en de imkerpraktijk.
Circadian rhythms in microalgae production
Winter, L. de - \ 2015
University. Promotor(en): Rene Wijffels, co-promotor(en): Maria Barbosa; Dirk Martens. - Wageningen : Wageningen University - ISBN 9789462573420 - 166
algen - circadiaan ritme - celdeling - lichtregiem - milieufactoren - biomassa productie - procesoptimalisatie - algae - circadian rhythm - cell division - light regime - environmental factors - biomass production - process optimization

Abstract Thesis: Circadian rhythms in microalgae production

Lenneke de Winter

The sun imposes a daily cycle of light and dark on nearly all organisms. The circadian clock evolved to help organisms program their activities at an appropriate time during this daily cycle. For example, UV sensitive processes, like DNA replication, can be scheduled to occur during the night (Nikaido and Johnson, 2000). In this way, the circadian clock causes rhythms in metabolic, physiological and/or behavioural events (Mittag et al., 2005). These circadian rhythms continue for some period of time following exposure to continuous light (Harding Jr et al., 1981) and have a duration of approximately 24 hours. In microalgae, circadian rhythms were observed in many processes, like nitrogen fixation, chemotaxis, photosynthesis and the cell division cycle (Mittag, 2001), which might affect the production of microalgae. Microalgae biomass can be used as source for potential biofuels, chemicals, materials, foods, feeds and high-value bioactives (Chisti, 2007; Hu et al., 2008; Wijffels and Barbosa, 2010). However, the current production process of microalgae needs to be optimized in order to become economically feasible (Norsker et al., 2011). Researchers focussed on optimizing PBR design (Molina et al., 2001; Morweiser et al., 2010; Sierra et al., 2008), operating strategies (Cuaresma et al., 2011; Morweiser et al., 2010; Olivieri et al., 2014) and microalgae metabolism (Guschina and Harwood, 2006; Klok et al., 2013a), but as of yet did not consider the possible influence of circadian rhythms on microalgae production.

Biomass growth rate, biomass yield on light, and the biochemical composition of algal biomass are important factors in the production of microalgae. These factors are likely to be influenced by the day/night cycle and the circadian clock. Therefore, the aim of the work presented in this thesis was to obtain more insight in circadian rhythms in microalgae grown in photobioreactors.

In chapter 2 it is described how the green microalgae Neochloris oleoabundans was grown in a photobioreactor operated as a turbidostat under continuous red LED light. Cell division in N. oleoabundans was shown to be under control of the circadian clock, and took place by multiple fission during the natural night. Due to the synchronized cell division, oscillations in biomass yield and composition were observed, despite the continuous red LED light. Synchronization disappeared under continuous white LED light, and therefore it was concluded that a blue light receptor might be involved in triggering synchronous cell division of N. oleoabundans.

As biomass composition is also dependent on other culture conditions, the same set-up was used in chapter 3, only this time the culture was grown nitrogen-limited, as this is the most commonly used method for the production of storage components. In this way, it was shown that under nitrogen limitation the circadian clock was still timing cell division to the natural night. However, because of the lower growth rate, two subpopulations were observed which divided alternately every other day. Again, oscillations in biomass composition were observed. Neutral lipids were built up during the day, especially in cells that were arrested in their cell cycle.

After having studied the circadian clock under continuous light conditions, a step was made to day/night cycles. Chapter 4 describes a comparison of biomass yield and composition between a synchronized culture under day/night cycles and a randomly dividing culture under continuous white LED light. In this way it was shown that circadian rhythms had a small influence on biomass yield, with biomass yield on light being 10-15% higher in synchronized cultures. Also biomass composition was influenced, as in continuous light starch never had to be spend for respiration during a dark period and therefore starch content remained higher. For the experiments with a day/night cycle, no difference was found between light supplied at constant intensity (block) or light supplied in a more natural way (sine). Therefore, providing light in a block showed to be a good and easy to operate alternative to using sinuses when working with day/night cycles in the laboratory.

Chapter 5 takes a closer look at the multiple fission cell cycle of N. oleaobundans. Day/night cycles of different lengths and intensities were studied, as algae are exposed to different day lengths over the course of a year. Maximum growth rate and start of starch synthesis seemed to be regulated by the circadian clock and were scheduled after approximately 6-7 hours from sunrise. Therefore, they were not influenced by day length. However, day length did have an influence on biomass composition. In longer days, more starch was accumulated. The changes in biomass composition could also be correlated to the cell cycle of N. oleoabundans, and therefore knowledge about the timing of cell division showed to be important for the production of biomass with a desired concentration of protein, lipids, carbohydrates or pigments.

In chapter 6 the implications of the overall results of this thesis for current research protocols and microalgae processes are discussed. First the occurrence of circadian rhythms in different species of microalgae is discussed, in order to establish the general nature of these rhythms. Based on the findings for N. oleoabundans, it is concluded that more research should be done using day/night cycles, as experiments under constant light are not representative for outdoor microalgae production. Still more knowledge is required on circadian rhythms in microalgae production and therefore some opportunities for future research are presented. Finally, it is discussed how manipulation of circadian rhythms might help to improve future microalgae production.

Interactie tussen varroa en omgevingsfactoren. Bijennieuws 28
Blacquière, T. ; Cornelissen, B. ; Dooremalen, C. van; Steen, J.J.M. van der - \ 2014
Wageningen : Bijen@wur
apidae - honingbijen - bijensterfte - doodsoorzaken - factoranalyse - milieufactoren - technieken - detectie - wetenschappelijk onderzoek - honey bees - bee mortality - causes of death - factor analysis - environmental factors - techniques - detection - scientific research
Het probleem van de sterfte van bijenvolken is multifactorieel. Allerlei factoren kunnen soms een beetje of soms zelfs sterk negatieve uitwerking hebben op bijenvolken, en die negatieve uitwerking kan in principe bijdragen aan de bijensterfte. Sommige factoren komen ook nog hand in hand (varroa en sommige virussen). Zolang de relatieve bijdrage van factoren niet bekend is kunnen we maar beter uitgaan van en rekening houden met een mogelijke bijdrage en ondertussen de factoren waar we alvast iets aan kunnen doen zo gunstig mogelijk te maken
Variatie en trend van de gehaltes zware metalen op locatie Zeelandbrug: Data rapport 2013
Schellekens, T. ; Glorius, S.T. ; Heuvel-Greve, M.J. van den - \ 2014
Yerseke : IMARES (Technisch rapport / IMARES Wageningen UR C055/14) - 26
oeverbescherming van rivieren - bekledingen - milieufactoren - milieueffect - mossels - ecotoxicologie - oosterschelde - riverbank protection - linings - environmental factors - environmental impact - mussels - ecotoxicology - eastern scheldt
Om erosie aan oevers van de Oosterschelde en Westerschelde tegen te gaan, is er in 2008 (pilot) en 2009 (structureel) begonnen om op die locaties waar deze erosie de stabiliteit van de waterkering in gevaar brengt of de reeds bestaande oeverwerken ondermijnt, ‘bestortingen’ uit te voeren om de oevers te beschermen. Deze bestortingen zijn uitgevoerd met staalslakken en breukstenen. Om met zekerheid vast te kunnen stellen dat er geen negatieve effecten optreden op het mariene milieu n.a.v. de oeververdediging is door Rijkswaterstaat besloten om een monitoringsprogramma op te zetten en uit te voeren.
Scherpere regels kunnen leiden tot smaller middelenpakket : Nieuwe toelatingsprocedure maant telers tot actie
Rodenburg, J. ; Os, E.A. van - \ 2014
Onder Glas 11 (2014)4. - p. 46 - 47.
glastuinbouw - gewasbescherming - normen - toelating van bestrijdingsmiddelen - milieufactoren - modificatie - verandering - emissie - greenhouse horticulture - plant protection - standards - authorisation of pesticides - environmental factors - modification - change - emission
De emissie van middelen en nutriënten uit kassen naar het oppervlaktewater ligt nog altijd ver boven de norm. Daarom gaat de toelatingsprocedure van gewasbeschermingsmiddelen in de glastuinbouw veranderen. Voor de substraatteelten komt er een meer op de praktijk gerichte milieurisicobeoordeling. Natuurlijk bestaat de angst dat de scherpere regels zullen leiden tot een smaller middelenpakket.
Metabolic adaptation of white adipose tissue to nutritional and environmental challenges
Hoevenaars, F.P.M. - \ 2014
University. Promotor(en): Jaap Keijer, co-promotor(en): Evert van Schothorst. - Wageningen : Wageningen University - ISBN 9789461739162 - 166
muizen - vetweefsel - metabolisme - adaptatiefysiologie - voeding - milieufactoren - obesitas - energieopname - zuurstoftekort - ontsteking - voedingsfysiologie - diermodellen - mice - adipose tissue - metabolism - adaptation physiology - nutrition - environmental factors - obesity - energy intake - oxygen deficiency - inflammation - nutrition physiology - animal models

Summary of main findings

When adipose tissue is present in excessive amounts, as in obesity, it predisposes to a number of pathologies. Obesity is a complex, multifactorial condition as it influences many endogenous genetic, endocrine, and inflammatory pathways. Excess dietary intake is one of the important factors which are responsible for the increasing prevalence of obesity. For the understanding of the reciprocity between

consumed diet and excessive amounts of adipose tissue, it is essential to investigate underlying functioning. In this thesis, I have addressed three important aspects that play a role in the development of diet induced obesity and its pathologies with a focus on adipose tissue metabolism.

Does a body weight set-point exist?

How is the diet-induced metabolic response affected by housing at


Does oxygen restriction induce inflammation in white adipose tissue?

The first aspect investigated was the existence of a body weight set point. A body weight set point is defined as a pre-determined or preferred level of body weight which is preserved by an internal feedback control mechanism. In chapter 2, a dietary intervention with none, one, or two diet alterations of purified diets was performed in C57BL/6J mice to investigate if a long lasting effect on body weight persistence was present. Diets contained equal protein content and source of ingredients but differed in the fat-to-sugar ratio. Therefore, energy content and amount of fat was different for either the low fat diet or the high fat. In the intervention the last consumed diet of the mice determined energy intake, energy expenditure, body weight, body fat stores, circulating hormones and metabolites. These data support the settling point theory as body weight and metabolic parameters ‘settle’ based on current energetic input and output and do not support the set point theory. Next to that it underlines the importance of diet choice in intervention studies focusing on aspects on the crossroads of nutrition and physiology.

In chapter 3adipose tissue physiology and molecular regulation was further investigated by exposure to more metabolic stress in the form of a weight loss challenge with different purified diets. Diet-induced obese C57BL/6J mice were fed a high fat diet restricted to 70% intake of previous ad libitum high fat diet

intake or they were changed to ad libitum low fat diet for 5 weeks. Beneficial effects were seen in both interventions regarding physiological parameters. However, molecular parameters in white adipose tissue differed between the two restriction interventions, with increased activation of mitochondrial carbohydrate and fat metabolism in high fat diet restricted mice. When extrapolated to the human

situation this may suggest that a reduction of portion size is the best method for weight loss.

It is standard practice to house mice at ambient temperature during physiological intervention studies. Unfortunately mice are then exposed to a temperature below their thermal neutral zone. This implies that their metabolism is chronically increased which is known to influence study outcomes. In chapter 4the second question; “how is the diet-induced metabolic response affected by housing at thermoneutrality?”was investigated. A 14-week dietary intervention with two semi-purified diets, a

low fat diet and a moderately high fat diet, was performed at 28°C in C57BL/6J mice. This resulted in a large diet-induced difference in bodyweight, adipose tissue mass, adipocyte size, and serum leptin level. But no differential effects of the diets were seen on serum glucose, free fatty acids, triacylglycerides, insulin, a panel of cardiovascular markers, and a number of (metabolic) parameters in liver and muscle.

Although adipose tissue mass and adipocyte size was increased significantly, there was no sign of inflammation or dysfunction in the adipose tissue. This study suggests that diet-induced obesity of C57BL/6J mice at thermoneutrality results in a suitable model for the metabolically ‘healthy’ obese (people who are significantly overweight but show none of the usual metabolic problems). Next to that, this study emphasizes the importance of consideration and control of housing temperature for mice, as it has profound effects on study outcomes.

The third and last question investigated was if oxygen restriction is able to induce inflammation in white adipose tissue. There is substantial evidence that white adipose tissue becomes hypoxic when excessively enlarged. Due to fast expansion of white adipose tissue the vasculature is not able to keep pace with growth. Next to that, adipocytes are able to increase in size beyond the limit of oxygen diffusion. To investigate if hypoxia was able to induce inflammation in white adipose tissue, the model for healthy obese adipocytes (developed in chapter 4) was used and exposed to ambient oxygen restriction (13%) to challenge adipose tissue metabolism. This resulted in the presence of systemic oxygen restriction as shown by increased levels of hemoglobin and hematocrit. Furthermore a switch to glycolytic metabolism, which is indicative for tissue hypoxia, was present. No differences in adipose tissue macrophage infiltration (as marker for inflammation) were found. But, serum branched chain amino acids and adipokines were affected. Branched chain amino acids were increased in mice exposed to oxygen restriction which shows resemblance with findings in humans where increased levels were found in lean versus obese people. The peptide hormone adiponectin was increased in serum, without differences in WAT expression. On the other hand, the peptide hormones CCDC3 and CCK showed decreased transcript levels in white adipose tissue without significant change in serum levels, although for CCDC3 a trend was seen. Together these results suggest that oxygen restriction does not induce inflammation in adipose tissue. However, it does affect adipokine regulation.

After performing these studies it was clear that composition of the diet has a major influence on outcome parameters of physiological studies as shown in chapter 2. To compare functional effects of different nutrients, it is important to use standardized purified diets. Not only the experimental intervention diet is of importance but also the reference control diet can influence outcomes. For example, when an intervention is performed with a high fat purified diet and the reference diet is chow this will lead to a difficult comparison. The content of chow is variable as it is grain or cereal based (ground corn, ground oats alfalfa meal, soybean meal and ground wheat). Nutritional adequacy is ensured by addition of vitamins, minerals, and fat. However, the exact amount of the various ingredients is frequently kept secret by the manufacturer. Next to that, due to the plant based origin of chow it will contain nutritive (protein, carbohydrate, fat) components but also non-nutritive components (phytochemicals). The content of the chow diet will vary from batch to batch as the nutritive and nonnutritive value will change between harvests. When using a chow reference diet in

comparison to a purified diet you will never know exactly what you are comparing, i.e. difference in amino acids or effects of phytochemicals etc. Therefore, a reference diet for physiology was designed (chapter 6) to improve comparison of study outcomes and to increase efficiency of resources and material. A key feature of the diet is the fixed protein concentration, which allows for an exchange of carbohydrate and fat in a high fat version of the diet.

To conclude, the work presented in this thesis provides clear insight in factors that are of importance for improvement of translatability of mouse studies to the human situation. It was shown that when investigating the weight balance many parameters, i.e. genetics, metabolic rate, environmental factors like ambient housing temperature and light and cognitive behavior, besides the diet and its composition are able to influence the outcome parameters. As most mouse experiments are performed

in a fixed environment with no choices of food and a standard temperature set to 22°C. This is clearly not reflective of humans under free living conditions. However, these fixed conditions are able to result in experiments that unravel underlying mechanisms of weight balance, which form the basis for discovering a solution to the obesity epidemic.

Actualisering ammoniakemissiefactoren rundvee: advies voor aanpassing in de Regeling ammoniak en veehouderij = Update of ammonia emission factors for cattle categories: advisory report for amendments in regulations on ammonia and livestock
Ogink, N.W.M. ; Groenestein, C.M. ; Mosquera, J. - \ 2014
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 744) - 29
rundveehouderij - mestbeleid - ammoniakemissie - huisvesting van rundvee - milieufactoren - cattle husbandry - manure policy - ammonia emission - cattle housing - environmental factors
The objective of this study is to update ammonia emission factors of cattle categories in the Regulation on ammonia and livestock in the Netherlands. The study evaluates the representativeness of emission factors for current management conditions and the availability of new information on emission. It is advised to increase the emission factor for conventional housing of dairy cattle (loose housing with slatted floors) and listed low emission housing systems by 18%.
'MeerWaarde uit Innoveren' : Kennis & Innovatieagenda Betuwse Bloem ’13-’15 : selectie thema’s en onderwerpen, uitgebreide rapportage
Werd, H.A.E. de; Schuur, L. ; Kloos, W. ; Pinxterhuis, E.K. - \ 2013
Randwijk : Praktijkonderzoek Plant en Omgeving, Bloembollen, Boomkwekerij & Fruit - 27
tuinbouw - tuinbouwbedrijven - innovaties - clusters - ondernemerschap - kennisoverdracht - economische samenwerking - logistiek - milieufactoren - biobased economy - voeding en gezondheid - betuwe - horticulture - market gardens - innovations - entrepreneurship - knowledge transfer - economic cooperation - logistics - environmental factors - nutrition and health
Dit document vormt de basis voor de kennis-en innovatieagenda Greenport Betuwse Bloem. De kennis- en innovatieagenda bestaat uit een overzicht met thema’s en onderliggende innovatie-onderwerpen waar ondernemers mee aan de slag willen. De selectie van thema’s en onderwerpen dient als startpunt voor innovatieprojecten met ondernemers. De beschrijving van de werkwijze voor selectie en prioritering van onderwerpen, kan gebruikt worden voor het selecteren en prioriteren van toekomstige onderwerpen met ondernemers.
Hoe stikstof de vlinders laat stikken
Wallis de Vries, M.F. - \ 2013
Entomologische Berichten 73 (2013)4. - ISSN 0013-8827 - p. 158 - 163.
lepidoptera - habitats - depositie - stikstof - natuurgebieden - terrestrische ecologie - milieufactoren - deposition - nitrogen - natural areas - terrestrial ecology - environmental factors
De verstoring van de stikstofkringloop door de mens, via de productie van kunstmest en via industrie en verkeer, wordt als één van de grootste bedreigingen beschouwd voor de ecologische stabiliteit van de aarde. De atmosferische depositie van stikstof dringt tot ver in de natuurgebieden door. De effecten op de biodiversiteit zijn voor planten al goed onderzocht, maar de doorwerking op de dierenwereld is nog goeddeels onbekend. Dit artikel belicht de invloed op dagvlinders. De meeste soorten daarvan komen in stikstofarme milieus voor. Bij deze groep overheerst de neerwaartse trend, in tegenstelling tot soorten van stikstofrijkere milieus. Ook de afname in aantallen vlinders blijkt sterker te zijn met toenemende stikstofdepositie. Drie mechanismen lijken daarbij een rol te spelen: afname van voedselplanten, afname van voedselkwaliteit en afkoeling van het microklimaat in het voorjaar.
Ultra-energiezuinige kassystemen met Supertransparante Micro-V Gestructureerde materialen: Rapportage in het kader van het EOS-LT programma van Agentschap NL (Openbare versie)
Gieling, T.H. ; Ruijven, J.P.M. van; Swinkels, G.L.A.M. ; Holterman, H.J. ; Mohammadkhani, V. ; Ruijs, M.N.A. ; Rijn, C.J.M. van; Baggerman, J. ; Rath, J.K. ; Jong, M. de; Schropp, R.E.I. - \ 2013
Wageningen : Wageningen UR Glastuinbouw (Rapporten Wageningen UR Glastuinbouw 1277) - 100
teelt onder bescherming - glastuinbouw - materialen - innovaties - lichtrelaties - optische eigenschappen - milieufactoren - schermen - kastechniek - protected cultivation - greenhouse horticulture - materials - innovations - light relations - optical properties - environmental factors - blinds - greenhouse technology
Doel van het in dit rapport beschreven onderzoek is het gebruiken van micro- en nanostructuren uit de PV-industrie om te komen tot een diffuus kasdekmateriaal met een hoge hemisferische transmissie. Hierbij wordt gebruik gemaakt van de kennis die in het verleden is opgedaan in het ontwikkelen van het zigzag kasdekmateriaal. Met de ontwikkelde kennis kan energiebesparing gerealiseerd worden door het toepassen van de structuren op dubbel glas, waardoor materiaal gemaakt kan worden met een hoge hemisferische transmissie, diffuse eigenschappen en een hoge isolatiewaarde. Randvoorwaarde hierin is dat het ontwikkelde kasdekmateriaal toepasbaar is in een glastuinbouwmilieu. Dit betekent dat het materiaal niet mag verouderen, condensatie de transmissie niet mag verminderen en extra vervuiling niet mag optreden. Hierbij wordt de Nederlandse situatie als uitgangspunt genomen, maar interessante structuren voor andere klimaten zullen niet worden uitgesloten.
Macrophytes in drainage ditches : functioning and perspectives for recovery
Zuidam, J.P. van - \ 2013
University. Promotor(en): Marten Scheffer, co-promotor(en): Edwin Peeters. - S.l. : s.n. - ISBN 9789461735898 - 112
sloten - aquatische ecologie - waterplanten - soortendiversiteit - milieufactoren - nutriëntenuitspoeling - polders - ecohydrologie - ecologisch herstel - drainage - baggeren - ditches - aquatic ecology - aquatic plants - species diversity - environmental factors - nutrient leaching - ecohydrology - ecological restoration - dredging
Sloten zijn overal ter wereld te vinden en vormen een belangrijk onderdeel van het Nederlandse landschap. Ondanks dat het door de mens gemaakte, kunstmatige wateren zijn, kunnen ze een grote diversiteit aan flora en fauna bevatten. Hierdoor dragen ze in belangrijke mate bij aan de biodiversiteit van het agrarisch landschap. Doordat sloten in ecologisch opzicht sterk lijken op afgesloten nevengeulen in rivieruiterwaarden zouden sloten zelfs een vervanger kunnen zijn voor de nevengeulen die op veel plaatsen zijn verdwenen. Verstoringen als eutrofiering en frequent vegetatie verwijderen hebben er echter voor gezorgd dat veel sloten momenteel een monocultuur bevatten van bijvoorbeeld kroos of Smalle waterpest (Elodea nuttallii). Deze monoculturen zorgen voor verslechterde leefomstandigheden voor waterdieren (vissen, amfibieën en ongewervelde dieren) waardoor de totale biodiversiteit van de sloot achteruit gaat. Om achteruitgang van de ecologische kwaliteit te voorkomen of terug te dringen is kennis nodig over de factoren die verantwoordelijk zijn voor het voorkomen van verschillende typen vegetatie. Het onderzoek in dit proefschrift richt zich daarom op het identificeren van condities en mechanismen die de samenstelling en het functioneren van watervegetaties in Nederlandse sloten bepalen, waarbij meer specifiek gekeken is naar de effecten van voedselrijkdom, onderhoud en de aanwezige overlevingsorganen.
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