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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Biotic interactions and trait-based ecosystem functioning in soil
Sechi, Valentina - \ 2017
University. Promotor(en): Lijbert Brussaard, co-promotor(en): Ron de Goede; C. Mulder; M. Rutgers. - Wageningen : Wageningen University - ISBN 9789463431316 - 176
soil - ecosystems - plant-animal interactions - interactions - soil biology - soil quality - grasslands - collembola - diversity - bodem - ecosystemen - plant-dier interacties - interacties - bodembiologie - bodemkwaliteit - graslanden - diversiteit

Recent emphasis on ecosystem services as a framework to evaluate ecosystems and to promote their sustainable use has drawn attention to how organisms contribute to the delivery of services. Soil attributes and biotic interactions play important roles in ecological processes (e.g. soil formation, nutrient turnover, carbon sequestration and transformation) and, consequently, in the related delivery of ecosystem services.

Therefore, understanding how soil organisms interact and how they respond to environmental conditions is fundamental to preserve soil functioning and provide a meaningful assessment of ecosystem services. Functional traits determine individual responses to pressures and their effects on ecosystem functioning hence, investigating soil ecosystems from a trait-based perspective offers an interesting opportunity to link the functional responses of the organisms to environmental pressures and to give insight into how the entire community influences ecological processes.

The main objective of this thesis is to develop and to test concepts for a trait-driven quantification of ecosystem services through the assessment of the effects of land management on soil processes. In particular, it focuses on exploring the potential of a trait-based approach in identifying and better understanding the response of the soil biota to environmental pressures and analyses the responses of soil organisms in terms of changes in functional trait distribution and trophic interactions.

This work shows that approaches taking the whole soil community into consideration are more suitable to give insight into the effect of anthropogenic pressure on ecosystem functioning than approaches based on single taxonomic groups. Moreover, performing combined analysis (e.g. analysing body-mass distribution and trophic grouping) helps to better identify community response to environmental pressure.

A clear methodology for the next step, i.e. quantification of ecosystem services, is still lacking due to the current difficulties to link and quantify the effect of anthropogenic pressure to ecosystem functioning in soil. For this reason, it is essential that methods analysed in this thesis will be further explored under different environmental pressures to enable the development of tools to be used at the interface of science and society for sustainable development.

Studying fast dynamics in biological complexes : from photosynthesis in vivo to single DNA molecules in vitro
Farooq, Shazia - \ 2017
University. Promotor(en): Herbert van Amerongen, co-promotor(en): Johannes Hohlbein. - Wageningen : Wageningen University - ISBN 9789463431002 - 149
biology - dna - proteins - interactions - probability analysis - förster resonance energy transfer - fluorescence - spectroscopy - photosynthesis - biologie - eiwitten - interacties - waarschijnlijkheidsanalyse - förster resonantie-energieoverdracht - fluorescentie - spectroscopie - fotosynthese

During the last decades, fluorescence spectroscopy has emerged as a powerful tool in the fields of biophysics, biotechnology, biochemistry, cellular biology and the medical sciences. These techniques are highly sensitive, and allow us to study the structure and dynamics of (bio)molecular systems (Valeur 2001). A significant advantage of fluorescence techniques is that they can often be non-invasive and measurements can be performed in real time. In this thesis different advanced fluorescence methods will be used to study two important biological processes: (1) DNA dynamics and (2) plant photosynthesis. The first part aims at improving the smFRET technique for the analysis of DNA dynamics and other fast conformational changes. This improvement is made by combining and developing instrumentation and data evaluation tools. The second part is the continuous development of time-resolved fluorescence spectroscopy methods, as well their application in the field of photosynthesis to study ultrafast processes in thylakoid membranes and leaves. The two fluorescence techniques are technically and conceptually very different, but they are both designed for analysis of biomolecular systems. In this thesis, the techniques are applied to study energy transfer and dynamical changes in DNAs, thylakoid membranes and leaves.

REFERENCE: VALEUR B 2001. Molecular Fluorescence: Principles and Applications. 1 ed: Wiley-VCH.

Bacteriophage: from exploration to exploitation
Nobrega, Franklin L. - \ 2017
University. Promotor(en): John van der Oost, co-promotor(en): J. Azeredo; Stan Brouns. - Wageningen : Wageningen University - ISBN 9789463430524 - 338
bacteriophages - hosts - interactions - genetic engineering - methodology - screening - bacteriofagen - gastheren (dieren, mensen, planten) - interacties - genetische modificatie - methodologie - screenen

Over the past decades, bacteriophage research has revealed the abundance of phages in nature, their morphological and genomic diversity, their influence in the regulation of microbial balance in the ecosystem and their impact on the evolution of microbial diversity. Since the 1950s, phages have also played a central role in some of the most significant fundamental discoveries in biological sciences that have been crucial for the development of molecular biology. More recently, phage research has resulted in the development of genome editing tools, and it has generated the renewed interest of using phages and phage-related products as therapeutic agents. Although major progress has been made, basic understanding on phage biology is still lacking. The number of phage genes with unknown function still largely outnumber those with established roles. Therefore, further progress depends on a deeper understanding on phage biology.

The present thesis aims at developing tools to support phage research, explores the use of phages for therapeutic purposes, and expands our insights into the biology of phages. A literature review on the molecular, structural and evolutionary determinants of phage-host interaction (Chapters 1 and 2) underlines the relatively poor understanding of the subject. A great variety of structures and mechanisms of infection are being revealed, but no correlations have yet been established between these and host interaction. Furthermore, so far no evolutionary model accurately describes the coevolution of phages and bacteria. A particular interest of evolutionary studies concerns the understanding of the prevalence of broad-host range phages in natural environments, since these are rarely isolated using standard laboratory isolation procedures. Indeed, we have tried to isolate broad host range phages targeting the Escherichia coli reference collection (Chapter 3), but found narrow-host range phages to be more prevalent. Only one phage of relatively broad host range was found (S2-36s), being able to infect 14 of the 72 strains. Proteins of interest for further exploration were found, such as depolymerases and colanic acid-degrading proteins, both with potential anti-biofilm activity.

The isolation procedures against the ECOR collection proved to be challenging due to the amount of strains and samples to be evaluated. Consequently, a high-throughput methodology was developed to simplify these isolation procedures (Chapter 4). By automated monitoring of cell growth in 96-well plates it is possible to use differences in optical densities (plotted as heatmaps) between cells subjected to the samples and in control conditions to screen for the presence of phages. The method revealed an accuracy of 98% and reduced the workload by 90%. The method developed can also be used to screen for broad-host range phages or to screen collections of phages for variants or cocktails that are suitable for treating bacterial infections. A discussion is provided of the advantages and limitations of phages for therapeutic applications (Chapter 5). It is suggested that phages in their natural state cannot be used in therapeutic applications. The future of phage therapy may possibly be genome engineering for tailoring of phage properties. Subsequently, the genetic modification of phage T7 was shown to improve (2-log) the capacity of the phage to resist to the strongly acidic conditions and enzymatic challenges of the gastrointestinal tract (Chapter 6). This was achieved by modifying the phage to express a signal peptide on its capsid to which phospholipids attach forming a protective coating. The removal of the phospholipid coating using phospholipase caused reversion to the pH-sensitive phenotype of the wild-type phage. In case of orally-delivered phages, this may improve the efficacy of phage therapy.

Engineering of phage genomes can also support evolutionary studies and basic phage research, e.g. analyzing if a certain gene is essential. A strategy developed for the random recombination of phage genomes (Chapter 7) demonstrated that it is possible to create novel productive phages by combining elements of different phage families. The findings reveal an unexpected level of flexibility and adaptability of phage genomes to accommodate and re-arrange genetic information, reflecting the pre-existing evolutionary compatibility of genes from different phages. The method is further expected to serve as a platform for improving our understanding of phage gene function and importance, where the random recombination of a single phage genome may be the preferred approach.

A different approach for the therapeutic application of phages was explored. Using phage display it was possible to identify peptides targeting claudin-low breast cancer cells (Chapter 8) and osteoarthritis cells (Chapter 9) with high levels of specificity. The peptides identified may contribute to an early detection of claudin-low breast carcinomas, and to develop more individualized therapies for both breast cancer and osteoarthritis.

In summary, the work developed in this thesis has resulted in new methodologies and biological data, thereby contributing to an increased understanding of phage biology and of the opportunities for the use of phages for diagnosis and therapy.

Interplay between gut microbiota and antibiotics
Jesus Bello Gonzalez, Teresita de - \ 2016
University. Promotor(en): Hauke Smidt; Mark van Passel. - Wageningen : Wageningen University - ISBN 9789463430043 - 293
antibiotics - intestinal microorganisms - aminoglycoside antibiotics - enterococcus - interactions - zoo animals - man - patients - dna sequencing - polymerase chain reaction - antibiotica - darmmicro-organismen - aminoglycoside antibiotica - interacties - dierentuindieren - mens - patiënten - dna-sequencing - polymerase-kettingreactie

The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria.

Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them.

The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence.

Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype. In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated.

Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosyl-hydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of non-human primates, the applicability of Human Intestinal Tract Chip (HITChip) to study the gut microbiota composition of these animals was assessed, including a comparison with healthy human volunteers (Chapter 3). It was concluded that the HITChip can be successfully applied to the gut microbiota of closely related hominids, and the microbiota dynamics can therefore be quickly assessed by the HITChip.

In Chapter 4, a combination of 16S rRNA phylogenetic profiling using the HITChip and metagenomics sequencing was implemented on samples from a single ICU hospitalized patient that received antibiotic prophylactic therapy (Selective Digestive Decontamination - SDD). The different approaches showed a highly dynamic microbiota composition over time and the prevalence of aminoglycoside resistance genes harbored by a member of the commensal anaerobic microbiota, highlighting the role of the commensal microbiota as a reservoir of antibiotic resistance genes. As an extension of this study (Chapter 5), 11 ICU patients receiving SDD were followed using 10 healthy individuals as a control group to compare the diversity and dynamics of the gut microbiota and resistome by HITChip and nanolitre-scale quantitative PCRs, respectively. The microbial diversity of the healthy individuals was higher compared to ICU patients, and it was less dynamic compared to ICU patients under antibiotic treatment. Likewise, the levels of antibiotic resistance genes increased in ICU patients compared to healthy individuals, indicating that during ICU hospitalization and the SDD, gut microbiota diversity and dynamics are profoundly affected, including the selection of antibiotic resistance in anaerobic commensal bacteria.

This was further expanded in an extensive study focusing on colonization dynamics with antibiotic resistant bacteria as described in Chapter 6. This was performed in the same group of ICU-hospitalized patients receiving SDD therapy and showed that by using a range of culture media and selective conditions a variety of taxonomic groups could be isolated, including aerobic and anaerobic antibiotic resistant bacteria. The overall composition of the faecal microbiota detected by HITChip indicated mainly a decrease of Enterobacteriaceae and an increase of the enterococcal population. Since critically ill patients are susceptible to hospital-acquired infections and the control of the emergence of antibiotic resistance is crucial to improve therapeutic outcomes, an extended analysis of the Enterococcus colonization dynamics in this group of patients by cultivation and phenotypic and genotypic characterization of the isolates provided new information about carriage of antibiotic resistance and virulence factor encoding genes (Chapter 7). It also highlighted the opportunity for the exchange of resistance and virulence genes, which could increase the risk of acquiring nosocomial infections.

Next, chapter 8 described the implementation of high-throughput cultivation-based screening using the Microdish platform combined with high-throughput sequencing (MiSeq) using faecal samples from ICU patients receiving SDD. This allowed for the recovery of previously uncultivable bacteria, including a pure culture of a close relative of Sellimonas intestinalis BR72T that was isolated from media containing tobramycin, cefotaxime and polymyxin E. This strain could therefore represent a potential antibiotic resistance reservoir.

In conclusion, this thesis provides broad insight into the diversity and dynamics of the gut microbiota and resistome in ICU hospitalized patients receiving SDD therapy as well as the dynamics of colonization with antibiotic resistant bacteria. Especially our extensive study of the colonization dynamics of Enterococcus spp. during ICU stay reinforced the notion that SDD therapy does not cover this group of bacteria and highlights the importance of a critical control of the emergence of antibiotic resistance in enterococci and their spread and dissemination as known potential pathogens.

Furthermore, the extensive use of antibiotics could select for an increase in the rate of antibiotic resistance against aminoglycosides and beta-lactams, indicating that a control in the use of broad spectrum antibiotics needs to be considered. In addition, this thesis provides evidence regarding the possible genetic background involved in the subsistence phenotype, however, future studies on metabolic pathways could provide novel insight into the underlying mechanisms.

Searching for balance : stability and equilibria of food webs
Altena, C. van - \ 2016
University. Promotor(en): Peter de Ruiter; J.A.P. Heesterbeek; Wolf Mooij, co-promotor(en): Lia Hemerik. - Wageningen : Wageningen University - ISBN 9789462576827 - 130 p.
food webs - models - interactions - ecology - biocoenosis - ecological balance - voedselwebben - modellen - interacties - ecologie - biocenose - ecologisch evenwicht


How complexity of food webs relates to stability has been a subject of many studies. Often,

unweighted connectance is used to express complexity. Unweighted connectance is

measured as the proportion of realized links in the network. Weighted connectance, on the

other hand, takes link weights (fluxes or feeding rates) into account and captures the shape

of the flux distribution. Here, we used weighted connectance to revisit the relation between

complexity and stability. We used 15 real soil food webs and determined the feeding rates

and the interaction strength matrices. We calculated both versions of connectance, and

related these structural properties to food web stability. We also determined the skewness

of both flux and interaction strength distributions with the Gini coefficient. We found no

relation between unweighted connectance and food web stability, but weighted connectance

was positively correlated with stability. This finding challenges the notion that complexity

may constrain stability, and supports the ‘complexity begets stability’ notion. The positive

correlation between weighted connectance and stability implies that the more evenly flux

rates were distributed over links, the more stable the webs were. This was confirmed by the

Gini coefficients of both fluxes and interaction strengths. However, the most even

distributions of this dataset still were strongly skewed towards small fluxes or weak

interaction strengths. Thus, incorporating these distribution with many weak links via

weighted instead of unweighted food web measures can shed new light on classical


The importance of phenology in studies of plant-herbivore-parasitoid interactions
Fei, Minghui - \ 2016
University. Promotor(en): Louise Vet; J.A. Harvey; Rieta Gols. - Wageningen : Wageningen University - ISBN 9789462576551 - 170 p.
016-3952 - phenology - plant-herbivore interactions - parasitoids - interactions - annuals - insects - pieris brassicae - cotesia glomerata - brassicaceae - host plants - fenologie - plant-herbivoor relaties - parasitoïden - interacties - eenjarigen - insecten - waardplanten
Genetic variation in plant chemistry : consequences for plant-insect interactions
Geem, Moniek van - \ 2016
University. Promotor(en): Wim van der Putten; J.A. Harvey, co-promotor(en): Rieta Gols. - Wageningen : Wageningen University - ISBN 9789462576681 - 141 p.
phytochemistry - plant composition - genetic variation - insect plant relations - interactions - defence mechanisms - soil biology - fytochemie - plantensamenstelling - genetische variatie - insect-plant relaties - interacties - verdedigingsmechanismen - bodembiologie

Plants form the basis of many food webs and are consumed by a wide variety of organisms, including herbivorous insects. Over the course of evolution, plants have evolved mechanisms to defend themselves against herbivory, whereas herbivorous insects have evolved counter-mechanisms to overcome these defences (a.k.a. co-evolutionary arms races). Plant-insect interactions are not restricted to plants and their herbivores (bi-trophic interactions), but also involve natural enemies of the herbivores such as parasitoids and predators (tri-trophic interactions). Plant quality can affect the quality of the host or prey for parasitoids and predators, respectively. In addition, other plant traits are important in providing shelter, alternative food sources, or chemical cues that can be used for host/prey location. Moreover, as plants reside in both soil and air, they mediate interactions between organisms above- and belowground through changes in plant quality. Plant quality is determined by secondary metabolites and morphological traits that may negatively affect the performance of insects, as well as by primary metabolites that plants produce in order to grow, develop and reproduce, which also provide essential nutrients for insects.

Natural plant populations often exhibit genetic variation in various plant traits that include, amongst others, primary and secondary chemistry. Genetic variation in plant defence traits, such as the production of secondary metabolites, can be under selection pressure from a suite of biotic and abiotic factors that vary in space and time. Herbivorous insects may encounter a wide range of plant metabolites because the total concentrations of primary and secondary metabolites and the concentrations of individual compounds vary between genetically different plants. Also as a consequence of genetic variation, plants can respond differently to herbivory in terms of induced defence chemistry and re-allocation of metabolites.

The main aim of this thesis was to study how genetic variation in plant chemistry affects (multi)trophic interactions between wild cabbage plants and associated insects, both above- and belowground. As a model system I used five naturally occurring populations of wild cabbage (Brassica oleracea) located in the Dorset area in the UK. These populations have been shown to genetically differ in their defence chemistry profiles even though they are located in relatively close proximity to each other. Wild cabbages belong to the Brassicaceae, a plant family that is characterized by the production of glucosinolates, a group of secondary metabolites. Together with the enzyme myrosinase they form the chemical defence system of Brassicaceous plants including wild cabbage. Glucosinolates and myrosinases are stored separately in plant tissues but upon tissue damage they come into contact with each other upon which the glucosinolates are hydrolysed into potentially toxic break down products. The wild cabbage populations used in this thesis differ in their total glucosinolate concentrations as well as in the expression of individual glucosinolates.

In chapter 1 I describe plant-insect interactions in a multi-trophic framework, including both the above- and belowground compartments. Genetic variation in plant traits is introduced as the main topic of this thesis, and I present the main aim and outline of my work.

In chapter 2 I discuss how aboveground-belowground interactions influence the evolution and maintenance of genetic variation in plant defence chemistry. I review literature on AG-BG interactions as selection pressures for genetic variation, discuss hypotheses about plant mediation of AG-BG interactions, identify gaps in our knowledge such as the influence of spatial-temporal variation in AG-BG interactions, and in the end present new data on genetic variation in secondary chemistry of wild cabbage and related species.

The co-evolutionary arms race between plants and insects has resulted in adaptations in herbivores to cope with plant defence traits. Some insect herbivore species concentrate or sequester secondary metabolites from their food plant and use them in defence against their own enemies. In chapter 3 I studied whether sequestration of glucosinolates by a specialist herbivore is an effective defence mechanism against a generalist predatory bug. I used the sequestering herbivore Athalia rosae as one prey species, and the non-sequestering herbivore Pieris rapae as the control prey species. I compared the performance of the predatory stink bug Podisus maculiventris on these two prey species. As an extra factor, the two prey species were each reared on three different wild cabbage populations to test if plant population would have an effect on the predator through the sequestering herbivore. I found no consistent effect of plant population on the performance of the predator, and prey species only marginally affected its performance. Based on the results I suggest that in some trophic interactions sequestration is not an effective defence mechanism but merely an alternative way of harmlessly dealing with plant secondary metabolites.

In addition to aboveground plant-insect interactions, belowground interactions were considered as well. To test whether the performance of the belowground specialist herbivore Delia radicum, of which the larvae feed on root tissues, was influenced by population-related variation in defence chemistry, I reared this species on the five wild cabbage populations (chapter 4). Chemical analyses of root tissues revealed that there were differences amongst the populations in plant primary (amino acids and sugars) and secondary (glucosinolates) chemistry, but this did not affect the performance of the root herbivore, suggesting that D. radicum is well adapted to a wide range of total concentrations and concentrations of individual metabolites.

Whereas in chapters 3 and 4 I only focused on one compartment (aboveground and belowground respectively), in chapter 5 I included both compartments in one experiment. I studied the effect of belowground herbivory by larvae of the root fly D. radicum on the performance of an aboveground multi-trophic food chain, and whether this effect differed among three wild cabbage populations. I found that belowground herbivory differentially affected the performances of a specialist aboveground herbivore, the diamondback moth Plutella xylostella, and its parasitoid, Cotesia vestalis, with the parasitoid being more affected than the herbivore. Their performance also differed between the wild cabbage populations, often in interaction with the presence/absence of the belowground herbivore. For both the above- and belowground herbivore I found correlations between performance and plant chemistry, which differed between the insect species and also between males and females.

In chapter 6 I discuss the results of my experiments in relation to other studies. I finish with a general conclusion about my work and provide some ideas for future studies that could contribute to our knowledge in the field of (multi)trophic above-belowground interactions with regard to genetic variation in plant chemistry.

In my thesis I show that genetic variation in plant chemistry can affect the outcome of above-belowground plant-insect interactions. Herbivores and higher trophic levels were differently affected by the wild cabbage populations, and this difference was also influenced by the location of herbivory (i.e. aboveground or belowground). In both chapter 4 and chapter 5 I found no strong, unidirectional links between plant chemistry and insect performance, suggesting that other metabolites may have played a role in the observed differential effects of the wild cabbage populations. I also show that sequestration of plant allelochemicals in some herbivores is an alternative way of harmlessly dealing with plant secondary metabolites instead of an effective defence mechanism against predators (chapter 3).

Supramolecular nanoparticle interactions and biomolecule detection
Oikonomou, M.E. - \ 2016
University. Promotor(en): Aldrik Velders. - Wageningen : Wageningen University - ISBN 9789462576605 - 158 p.
nanotechnology - particles - nuclear magnetic resonance spectroscopy - supramolecular chemistry - lectins - interactions - nanotechnologie - deeltjes - kernmagnetische resonantiespectroscopie - supramoleculaire chemie - lectinen - interacties

Manipulating and understanding matter at the nanoscale describes best the interdisciplinary field of nanotechnology. Nanotechnology is entering, a new era, which is described by Jean-Marie Lehn as the era of “complex matter”. Complex matter is the combination of nanomaterials that together give rise to superstructures, “structures beyond nanostructures”. In this thesis, the motivation was to progressively discover and understand molecular interactions that govern nanoscale natural systems and beyond, and the goal was to acquire the ability to design, direct and control complex matter. In this context, supramolecular ligand interactions on nanoparticle surfaces were designed and implemented with an emphasis on biomolecule sensing. Three main topics were addressed:

1. NMR as a tool in Nanotechnology to study reactions and supramolecular interactions between molecules, nanoparticles and biomacromolecules.

2. Supramolecular Orthogonal Interactions at nanoparticle surfaces.

3. Applications of Supramolecular Orthogonal Interactions for biomolecule recognition and sensing.

Host-interaction effector molecules of Lactobacillus plantarum WCFS1
Lee, I.C. - \ 2016
University. Promotor(en): Michiel Kleerebezem, co-promotor(en): P.A. Bron. - Wageningen : Wageningen University - ISBN 9789462576858 - 183 p.
lactobacillus plantarum - molecules - probiotics - immunomodulatory properties - lipoproteins - interactions - molecular interactions - host pathogen interactions - moleculen - probiotica - immunomodulerende eigenschappen - lipoproteïnen - interacties - moleculaire interacties - gastheer-pathogeen interacties


Lactobacillus plantarum is found in various environmental habitats, including fermentation products and the mammalian gastrointestinal tract, and specific strains are marketed as probiotics, which are defined as ‘live microorganisms which when administered in adequate amounts confer a health benefit on the host’. Throughout the studies of the mechanisms underlying probiotic activity, it became apparent that the probiotic effects are often species and/or strain specific. This situation has led more researchers to focus on the molecular characteristics of probiotic strains intending to link specific molecular structures to specific probiotic functions, and thereby deduce the mechanisms of molecular communication of probiotics. This thesis focuses on potential cell envelope effector molecules involved in interaction with the mammalian host cells, including lipoteichoic acid (LTA), lipo- and glyco-proteins, and extracellular polysaccharides (EPS), of L. plantarum WCFS1, a model strain for probiotic lactobacilli with a well-annotated genome sequences and sophisticated genetic engineering tools. First, existing research regarding the potential roles in probiotic functionality of Lactobacillus surface molecules in terms of their biosynthesis pathways and structure variations as well as interaction with host Pattern Recognition Receptors (PRRs) and immunomodulatory properties of these molecules are summarized and compared to provide an overview of the state-of-the-art in probiotic effector molecule research. Subsequently, specific molecules that reside in the cell envelope of L. plantarum WCFS1 were study for their role in bacterial physiology, as well as their role as ligands in Toll-like receptor (TLR) 2 signaling and immunomodulatory properties using human-cell co-incubation models. Our results showed that the deficiency of LTA had a drastic impact on cell division, cell morphology and growth in L. plantarum WCFS1, while LTA-deficient cells also elicited more pro-inflammatory responses in PBMCs rather than the expected loss of pro-inflammatory capacity as was observed with similar mutants of Lactobacillus acidophilus NCFM. Further studies on the signaling capacity of the purified LTA from L. plantarum WCFS1 revealed that these molecules are poor TLR2 activators, which is in clear contrast to the highly potent TLR2 stimulatory capacity of LTA obtained from Bacillus subtilis, implying that structural differences of the LTA produced by different bacteria are prominent determinants of their TLR2 signaling capacity and immunomodulatory properties. Lipoproteins of L. plantarum WCFS1 were studied using a derivative strain that is deficient in prolipoprotein diacylglyceryltransferase (Lgt), which transfers acyl chain moieties onto lipoproteins. The lipid moiety was shown to be important for proper anchoring of lipoproteins and TLR1/2 signaling capacity, but did not affect TLR2/6 signaling, suggesting that lipoproteins of L. plantarum WCFS1 are predominantly (if not exclusively) triacylated. The Lgt deficient strain elicited more pro-inflammatory responses in PBMCs as compared to the wild type, indicating that the native lipoproteins could play a role in dampening inflammation upon host-probiotic interaction. In addition, we explored the protein glycosylation machinery in L. plantarum WCFS1, responsible for the glycosylation of the major autolysin (Acm2) of this bacterium, which was previously shown to be O-glycosylated with N-acetylhexosamine conjugates. Using sequence similarity searches in combination with a lectin-based glycan detection and mass spectrometry analysis, two glycosyl-transferases, GtfA and GtfB (formerly annotated as TagE5 and TagE6, respectively), were shown to be required for the glycosylation of Acm2 and other unidentified L. plantarum WCFS1 glycosylated proteins. These results provide the first example of a general protein-glycosylation machinery in a Lactobacillus species. Finally, extracellular polysaccharides (EPS) in L. plantarum were studied in two strains that produce large amounts of EPS: L. plantarum SF2A35B and Lp90, in comparison to the lowly producing model strain WCFS1. Based on genome sequence comparison, both of the high producer strains were found to possess strain-specific and unique polysaccharide gene clusters. These gene clusters were deleted and the mutants were shown to have lost the capacity to produce large amounts of EPS, and were studied in relation to their properties in host-bacteria interaction. The results illustrate strain-specific and variable impacts of the removal of the EPS in the background of individual L. plantarum strains, supporting the importance of EPS in L. plantarum strains as a strain-specific determinant in host interaction. Overall, this thesis showed that surface molecules not only play important roles in bacterial physiology, but also in the interaction with the host mucosa through pattern recognition receptors expressed by the host cells. With the growing amount of evidence of structural variations in surface molecules, which are influenced by genetic background, physiological status, environmental factors, and other biological processes, these molecules form a unique signature associated with each strain that as a consequence elicits a strain-specific response when interacting with host cells.

Inzicht en Zichtbaar Weerbaar: meetmethoden nodig voor teelt-zeker weerbaar telen
Wurff, A.W.G. van der; Streminska, M.A. ; Boer, F.A. de; Cuesta Arenas, Y. ; Janse, J. - \ 2015
Wageningen UR
cropping systems - horticulture - plant protection - hydroponics - greenhouse horticulture - conferences - chrysanthemum - soilless culture - substrates - measurement - interactions - markers - plant development - climate - cultivars - tuinbouw - glastuinbouw - teeltsystemen - cultuur zonder grond - substraten - meting - interacties - merkers - plantenontwikkeling - klimaat
Aandacht wordt geschonken aan: voedingswater, micro-leven, rasverschillen, en oud stekmateriaal. Poster van PlantgezondheidEvent 12 maart 2015.
Eutrophication, Nile perch and food-web interactions in south-east Lake Victoria
Cornelissen, I.J.M. - \ 2015
University. Promotor(en): Johan Verreth, co-promotor(en): Leo Nagelkerke; R. Vijverberg. - Wageningen : Wageningen University - ISBN 9789462575660 - 163
lates niloticus - eutrofiëring - voedselwebben - interacties - visserijbiologie - visstand - dynamica - fytoplankton - distributie - voedingsgedrag - victoriameer - tanzania - eutrophication - food webs - interactions - fishery biology - fish stocks - dynamics - phytoplankton - distribution - feeding behaviour - lake victoria

The increasing eutrophication, the introduction of Nile perch (Lates niloticus) and the increasing fishing pressure has changed Lake Victoria tremendously the last century. Since the 1960s, eutrophication increased primary production, enabling an increase in fish production. However, eutrophication also created hypoxia pockets, which reduced the available habitats for fish. In addition, the endemic haplochromines declined, whereas the introduced Nile perch boomed in the 1980s. The Nile perch boom and increased fish production resulted in the largest freshwater fisheries of the world. However, it is unclear whether fish production can still increase with further eutrophication as maximum primary production rates may have been reached. Fish stocks fluctuate since the 1980s and in order to manage these, it is important to understand how eutrophication and fisheries affect the Nile perch population. The present study investigates the bottom-up effects of eutrophication on the Nile perch and food-web dynamics in south-east Lake Victoria. We analysed the level of eutrophication along an eutrophication gradient in the Mwanza Gulf. Phytoplankton biomass varied spatially and seasonally and was limited by nutrients in deep water and by light in shallow water. Fish distributions were dynamic, with environmental factors depth and temperature influencing Nile perch size structure and distribution patterns similarly on small and large spatial scales. Although prey densities of haplochromines and Caridina nilotica shrimp did not explain Nile perch distributions, ontogenetic diet shifts and composition were related to prey densities, suggesting an opportunistic feeding behaviour of Nile perch. Small Nile perch however, showed some preference to shrimp and Nile perch preferred haplochromines above Dagaa (Rastrineobola argentea) and juvenile Nile perch as fish prey. On a food-web level, the base of the food web was spatially and seasonally highly dynamic. The onset of rains caused a spatial differentiation in littoral/benthic and pelagic carbon sources, affecting the whole food web. Trophic levels of fish were related to the spatial variation in diet compositions. Although a large heterogeneity was found in water quality, fish distributions and food-web structure, bottom-up processes affected the food web similarly. Despite the ongoing nutrient load in Lake Victoria, water quality has improved since the 1990s. Climate forcing through increasing wind speeds increased visibility and oxygen levels. Global climate change will therefore be an important driver of the water quality and fish distributions of Lake Victoria.

Indirect genetic effects for group-housed animals
Alemu, S.W. - \ 2015
University. Promotor(en): Johan van Arendonk, co-promotor(en): L.G. Janss; Piter Bijma; P. Berg. - Wageningen : Wageningen University - ISBN 9788793176713 - 228
nerts - pluimvee - groepshuisvesting - genetische effecten - sociaal gedrag - agressief gedrag - interacties - heritability - veredelingsprogramma's - statistische analyse - genetische parameters - selectief fokken - mink - poultry - group housing - genetic effects - social behaviour - aggressive behaviour - interactions - breeding programmes - statistical analysis - genetic parameters - selective breeding


Alemu, SW(2015) Indirect Genetic effects for Group-housed Animals. Joint PhD thesis between Aarhus University, Denmark and Wageningen University, the Netherlands.

Social interactions among individuals are common both in plants and animals. With social interactions, the trait value of an individual may be influenced by the genes of its interacting partners, a phenomenon known as indirect genetic effects (IGE). An IGE is heritable effect of an individual on trait values of another individual. A large body of literature has shown that social interactions can create addition heritable variation in both plants and animals, for both behavioural and production traits.

When IGE are estimated it is usually assumed that an individual interacts equally with all its group mates, irrespective of genetic relatedness. This assumption may not be true in mixed groups of kin and non-kin, where an individual may interact systematically different with kin and non-kin. Current IGE models ignore such systematically different interactions between kin and non-kin. Thus, the main aim of this thesis was to develop and apply statistical methods to estimate IGE when interactions differ between kin and non-kin.

Social interactions are important in mink that are kept in groups for the production of fur. Group housing of mink increases aggression behaviours, which is reflected by an increase in the number of bite marks on the pelts, and reduces the welfare of the animals. We estimated the genetic parameter for bite mark traits in group-housed mink, to investigate the prospects for genetic improvement of bite mark traits. We found that there are good prospects to produce mink that have a low level of biting. Finally, we further concluded that genetic parameter estimation for bite mark score should take into account systematic interactions due to sex or kin.

In this thesis we also investigated genomic selection for socially affected traits, considering survival time in two lines of brown egg layers showing cannibalistic behaviour. Despite the limited reference population of ~234 progeny tested sires, the accuracy of estimated breeding values (EBV) was ~35% higher for genomic selection compared with the parent average-EBV. We found that the response to genomic selection per year for line B1 was substantially higher than for the traditional breeding scheme, whereas for line BD response was slightly higher than for the traditional breeding scheme. In conclusion, genetic selection with IGE combined with marker information can substantially reduce detrimental social behaviours such as cannibalism in layers and biting in group-housed mink.

Plant reageert traag op verandering van lichtsterkte : Enzym Rubisco staat vaak op de rem
Kaiser, E. ; Heuvelink, E. ; Kierkels, T. - \ 2014
Onder Glas 11 (2014)12. - p. 20 - 21.
glastuinbouw - plantenontwikkeling - kassen - diffuus glas - lichtsterkte - fotosynthese - interacties - groenten - proeven - greenhouse horticulture - plant development - greenhouses - diffused glass - light intensity - photosynthesis - interactions - vegetables - trials
De laatste jaren groeit het inzicht in de manier waarop planten reageren op het licht sterk. Om steekhoudende uitspraken te kunnen doen wordt het onderzoek uitgevoerd bij constante omstandigheden. Maar in een kas wisselt de lichtsterkte juist voortdurend. Hoe gaat de plant daarmee om?
Natural nanoparticles in soils and their role in organic-mineral interactions and cooloid-facilitated transport
Regelink, I.C. - \ 2014
University. Promotor(en): Rob Comans, co-promotor(en): Liping Weng. - Wageningen : Wageningen University - ISBN 9789462571501 - 221
bodem - bodemchemie - interacties - colloïden - transportprocessen - deeltjes - soil - soil chemistry - interactions - colloids - transport processes - particles

Mineral nanoparticles are naturally present in the soil and play an important role in several soil processes. This thesis uses a combination of novel analytical techniques, among which Field-Flow-Fractionation, to study nanoparticles in soil and water samples. The results show that nanoparticles can be as small as a few nanometer only and play an important role in the transport of phosphorus and trace metals in the environment. Furthermore, Fe-(hydr)oxide nanoparticles play an important role in sequestration of organic matter and phosphate in soils. The adsorption interactions between phosphorus and organic matter have important implications for the predictions of phosphorus-fertility status of the soil because phosphorus becomes more soluble in soils rich in organic matter. Moreover, this thesis shows that Fe-(hydr)oxide nanoparticles form strong aggregates with organic matter and thereby improve aggregate stability and water retention in soils.

Blowing the seeds of innovation: How scaling unfolds in innovation processes towards food security and sustainable agriculture
Potters, J.I. ; Berg, J. van den; Wolf, P.L. de; Lee, J. van der; Giani, A. ; Floquet, A. ; Vellema, S. ; Wigboldus, S. - \ 2014
Wageningen UR
duurzame landbouw - innovaties - voedselzekerheid - best practices - samenwerking - schaalverandering - processen - interacties - sustainable agriculture - innovations - food security - cooperation - scaling - processes - interactions
Many policy makers, business partners and researchers often think about innovations related to sustainable agriculture as the natural outcome of best practices and that scaling can be easily done once it becomes the responsibility of some manager or engineer. However, work done by researchers from Wageningen UR found that the scaling of innovations has tended to be an unpredictable, complex process, depending on the interactions between the 'DNA' of the innovation and the context within which it is taking place.
Food proteins as potential carriers for phenolics
Bohin, M.C. - \ 2013
University. Promotor(en): Harry Gruppen, co-promotor(en): Jean-Paul Vincken. - S.l. : s.n. - ISBN 9789461736765 - 140
eiwitten - fenolverbindingen - caseïne - caseïnaten - bitterheid - interacties - proteins - phenolic compounds - casein - caseinates - bitterness - interactions

The development of phenolic-rich functional foods is often limited by the off-tastes of phenolics that might be counteracted by sequestering these compounds using a carrier, thereby preventing them to interact with bitter taste receptors and salivary proteins. A range of common animal food proteins were tested for binding of phenolics. It appeared that a proline-rich open protein structure, as in β-casein, favored binding of phenolics. Globular proteins other than bovine serum albumin showed poor potential for use as carrier. No appropriate carriers for monomeric phenolics were found. β-Casein and Na-caseinate were shown to have good bitter-masking potential for EGCG, as measured by a maximal reduction in bitter receptor activation of ~93% measured in vitro. This effective reduction in bitter receptor activation was confirmed by a sensory test. This illustrates the validity of using food proteins with good binding properties as carriers for phenolics.

Different methodologies for probing the interaction between proteins and phenolics were developed: (i) ultrafiltration followed by UV quantification of unbound phenolics in the retentate, (ii) fluorescence quenching, and (iii) ultrafiltration followed by mass spectrometric quantification of unbound phenolics in the retentate. The latter method offered the opportunity to analyze preferential binding to protein of individual phenolics present in a complex mixture. With these methods, it was established that, with respect to phenolics, conformation and flexibility were important drivers of protein-phenolic interaction, besides degree of polymerization and galloylation. With respect to relatively proline-poor unstructured proteins such as α-casein and β-casein, it appeared that there should be other factors, besides proline density, explaining the interaction with phenolics.

On the modulation of innate immunity by plant-parasitic cyst nematodes
Postma, W.J. - \ 2013
University. Promotor(en): Jaap Bakker, co-promotor(en): Geert Smant; Aska Goverse. - S.l. : s.n. - ISBN 9789461735560 - 154
plantenparasitaire nematoden - globodera rostochiensis - heterodera schachtii - planten - interacties - immuniteit - immuunsysteem - modulatie - receptoren - signaaltransductie - moleculaire plantenziektekunde - plant parasitic nematodes - plants - interactions - immunity - immune system - modulation - receptors - signal transduction - molecular plant pathology

Plant-parasitic cyst nematodes are major agricultural pests worldwide. These obligate endoparasites invade the roots of host plants where they transform cells near the vascular cylinder into a permanent feeding site. Plants possess a multilayered innate immune system consisting of different types of extracellular and intracellular immune receptors. These enable detection of most invading nematodes and initiate immune responses that result in resistance. Many plant pathogens use effectors to overcome resistance. Here, modulation of plant innate immunity by plant-parasitic cyst nematodes was investigated. Extracellular immune receptor signaling and hormone-mediated signaling pathways were found to contain infection of susceptible Arabidopsis thalianawith Heterodera schachtii. A large family of effectors was identified in Globodera rostochiensis. One of these so-called SPRYSECs interacted with a novel CC-NB-LRR type resistance protein of a susceptible tomato without inducing resistance responses. Instead, the effector was found to suppress defense-related programmed cell death and resistance mediated by several CC-NB-LRR type resistance proteins. In addition, a secreted antimicrobial peptide was identified in G. rostochiensis. Plant-parasitic cyst nematodes thus most likely secrete effectors that protect against plant immune responses and secondary infections. The current evidence for the existence of immune modulating effectors is reviewed and directions for further research are given.

Tackling complex models in systems biology
Apri, M. - \ 2013
University. Promotor(en): Jaap Molenaar, co-promotor(en): Maarten de Gee. - S.l. : s.n. - ISBN 9789461735249 - 130
systeembiologie - modellen - biologie - wiskundige modellen - biologische processen - interacties - celcyclus - systems biology - models - biology - mathematical models - biological processes - interactions - cell cycle

One of the main obstacles in systems biology is complexity, a feature that is inherent to living systems. This complexity stems both from the large number of components involved and from the intricate interactions between these components. When the system is described by a mathematical model, we frequently end up with a large nonlinear set of mathematical equation that contains many parameters. Such a large model usually has a number of undesirable properties, e.g., its dynamical behavior is hard to understand, its parameters are difficult to identify, and its simulation requires a very long computing time. In this thesis, we present several strategies that may help to overcome these problems. On the level of method development, we focus on two issues: a) method development to analyze robustness, and b) method development to reduce model complexity. On the level of practical systems biology, we develop and analyze a model for the cell cycle in tomato fruit pericarp.

Robustness, that is the ability of a system to preserve biological functionality in spite of internal and external perturbations, is an essential feature of a biological system. Any mathematical model that describes this system should reflect this property. This implies the needs of a mathematical method to evaluate the robustness of mathematical models for biological processes. However, assessing robustness of a complex non-linear model that contains many parameters is not straightforward. In this thesis, we present a novel method to evaluate the robustness of mathematical models efficiently. This method enables us to find which parameter combinations in a model are responsible for its robustness. In this way, we get more insight into the underlying mechanisms that govern the robustness of the biological system. The advantage of our method is that the effort to apply the method scales linearly with the number of parameters. It is therefore very efficient when it is applied on mathematical models that contain a large number of parameters.

The complexity in a model can be brought down by simplifying the model. In this thesis, we also present a novel reduction method to simplify mathematical representations of biological models. In this method, biological components and parameters that do not contribute to the observed dynamics are considered redundant and hence are removed from the model. This results in a simpler model with less components and parameters, without losing predictive capabilities for any testable experimental condition. Since the reduced model contains less parameters, parameter identification can be carried out more efficaciously.

In the last part of this thesis we show how modeling can help us in understanding the cell cycle in tomato fruit pericarp. The cell cycle in this system is quite unique since the classical cell cycle, in which the cell division takes place, after some periods turns into a partial cycle where the cell keeps replicating its DNA but skips the division. Several mechanisms that are putatively responsible for this transition have been proposed. With modeling, we show that although each of these putative mechanisms could lead on its own the cell cycle to this transition, also their combination could lead to the same result. We also show that the mechanisms that yield the transition are very robust.

Gerichtere sturing van de oppervlaktewaterkwaliteit
Roelsma, J. ; Tol - Leenders, T.P. van; Dries, A. ; Dongen, M. van - \ 2012
H2O : tijdschrift voor watervoorziening en afvalwaterbehandeling 45 (2012)10. - ISSN 0166-8439 - p. 31 - 34.
oppervlaktewater - oppervlaktewaterkwaliteit - fosfor - mestbeleid - eutrofiëring - interacties - grondwater - bodemwater - bodemkwaliteit - hydrologie van stroomgebieden - drenthe - surface water - surface water quality - phosphorus - manure policy - eutrophication - interactions - groundwater - soil water - soil quality - catchment hydrology
De fosforconcentraties in het oppervlaktewater stijgen in de door landbouw gedomineerde delen van de Drentsche Aa ondanks de flinke afname van het gebruik van meststoffen door het aangescherpte mestbeleid. In het project Monitoring Stroomgebieden is in detail gekeken naar de relatie tussen het mestbeleid en de oppervlaktewaterkwaliteit. De stijgende trend in delen van het stroomgebied van de Drentsche Aa kan worden verklaard door de toegenomen fosfaatverzadiging van de landbouwbodems in combinatie met toename van neerslag en hogere grondwaterstanden. Door bij de interpretatie van de oppervlaktewatermetingen beter gebruik te maken van de informatie uit het bodemkwaliteitsmeetnet kan zeer gericht worden gestuurd op een goede oppervlaktewaterkwaliteit.
Flickering gives early warning signals of a critical transition to a eutrophic lake state : Letter
Wang, R. ; Dearing, J. ; Langdon, P.G. ; Zhang, E. ; Yang, X. ; Dakos, V. ; Scheffer, M. - \ 2012
Nature 492 (2012). - ISSN 0028-0836 - p. 419 - 422.
aquatische ecologie - oppervlaktewaterkwaliteit - meren - eutrofiëring - algen - toestandsverandering - overgangselementen - interacties - china - aquatic ecology - surface water quality - lakes - eutrophication - algae - change of state - transition elements - interactions - ecosystem services - regime shifts - climate-change - tipping point - resilience - systems - science - time
There is a recognized need to anticipate tipping points, or critical transitions, in social–ecological systems1, 2. Studies of mathematical3, 4, 5 and experimental6, 7, 8, 9 systems have shown that systems may ‘wobble’ before a critical transition. Such early warning signals10 may be due to the phenomenon of critical slowing down, which causes a system to recover slowly from small impacts, or to a flickering phenomenon, which causes a system to switch back and forth between alternative states in response to relatively large impacts. Such signals for transitions in social–ecological systems have rarely been observed11, not the least because high-resolution time series are normally required. Here we combine empirical data from a lake-catchment system with a mathematical model and show that flickering can be detected from sparse data. We show how rising variance coupled to decreasing autocorrelation and skewness started 10–30 years before the transition to eutrophic lake conditions in both the empirical records and the model output, a finding that is consistent with flickering rather than critical slowing down4, 12. Our results suggest that if environmental regimes are sufficiently affected by large external impacts that flickering is induced, then early warning signals of transitions in modern social–ecological systems may be stronger, and hence easier to identify, than previously thoug
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