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Biotic interactions and trait-based ecosystem functioning in soil
Sechi, Valentina - \ 2017
Wageningen 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
Wageningen 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
Wageningen 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
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): M.W.J. 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
Wageningen 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
Wageningen 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
Wageningen 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
Wageningen 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
Wageningen 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
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
Wageningen 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
Wageningen 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
Wageningen 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
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
Wageningen 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
Wageningen 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
Wageningen 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
Strengthening institutions or institutionalising weaknesses? : interactions between aid and institutions in Huíla Province, Angola
Serrano, M.M. - \ 2012
Wageningen University. Promotor(en): Thea Hilhorst. - [S.l.] : s.n. - ISBN 9789461731289 - 310
interventie - humanitaire hulp - ontwikkelingsprojecten - instellingen - plaatselijk bestuur - angola - afrika - interacties - intervention - humanitarian aid - development projects - institutions - local government - africa - interactions
This research analyses the interaction between aid interventions and local institutions through which people address needs during crisis. These include state and non- state institutions involved in social assistance and in the delivery of basic services such as healthcare. The study focuses on the case of Angola’s conflict, which lasted from independence in 1975 until 2002. It discusses aid policy and practice during the war and in the post-war context by examining various types of aid interventions and how they unfold on the ground. It shows that during the emergency, humanitarian practice largely ignored or bypassed local institutions. However, strengthening institutional capacity has become an explicit objective of post-conflict aid interventions. This thesis analyses the main types of institution-building interventions that have dominated Angola’s reconstruction period. It shows that these are strongly shaped by the legacy of relief practices on the legitimacy of local institutions, and on the functioning of the aid system. As a result, aid interventions rather than strengthening local institutions, often institutionalise their weaknesses.
Models to relate species to environment: a hierarchical statistical approac
Jamil, T. - \ 2012
Wageningen University. Promotor(en): Cajo ter Braak. - S.l. : s.n. - ISBN 9789461731395 - 146
statistiek - lineaire modellen - interacties - kenmerken - bayesiaanse theorie - plantenecologie - biostatistiek - statistics - linear models - interactions - traits - bayesian theory - plant ecology - biostatistics
In the last two decades, the interest of community ecologists in trait-based approaches has grown dramatically and these approaches have been increasingly applied to explain and predict response of species to environmental conditions. A variety of modelling techniques are available. The dominant technique is tocluster the species based on their functional traits and then summarize the response of the clusters to environmental change. In general, fitting explicit models to data is always more informative and powerful than more informal approaches. The central theme of the thesis is how to quantify the relation of traits with the environment using three data tables, data on species occurrence and abundance in sites, data on traits of species and data on the environmental characteristics of sites. In this thesis, we place the challenge of quantifying trait-environment relationships in the context of species distribution modelling, so in the context of species-environment relationships. We present a hierarchal statistical approach to species distribution modelling that efficiently utilize the trait information and that is able to automatically select the relevant traits and environmental characteristics. This model-based approach, coupled with recent statistical developments and increased computing power, opens up possibilities that were unimaginable before.
In the present study a hierarchical statistical approach is introduced for modeling and explaining species response along environmental gradients by species traits. The model is an extension of the generalized linear model with random terms that express the between-species variation in response to the environment. This so-called generalized linear mixed model (GLMM)is derived byintegrating a two-step procedure into one. As the basic GLMM we take the random intercept and random slope model. To introduce traits, the regression parameters (intercept and slope) are made linearly dependent on the species traits. As a consequence the trait-environment relationship is represented as an interaction term in the model. The method is illustrated using the famous Dune Meadow Data using Ellenberg indicator values as species traits.
Niche theory proclaims that species response to environmental gradients is nonlinear. Each species has preferred an environmental condition in which it can survive and reproduce optimally. Thus each species tends to be most abundant around a specific environmental optimum and the distribution of species along any environmental gradient is usually unimodal, with the maximum at some ecological optimum.For presence-absence data, the simplest unimodal (non-negative) species response curve is the Gaussian logistic response curve with three parameters that characterize the niche: optimum (niche centre), tolerance (niche width) and maximum (expected occurrence at the centre). Niches of species differ between species and species are assumed to be evolutionary adapted. It is difficult to fit the Gaussian logistic model with linear trait submodels for the parameters with the available (generalized) nonlinear mixed model software.
We develop the trait-modulated Gaussian logistic model in which the niche parameters are made linearly dependent on species traits. The model is fitted to data in the Bayesian frameworkusing OpenBUGS (Bayesian inference Using Gibbs Sampling).A Bayesian variable selection method is used to identify which species traits and environmental variables best explain the species data through this model. We extended the approach to find the best linear combination of environmental variables.
We explained why and when (generalized) linear mixed models can effectively analyse unimodal data and presented a graphical tool and statistical test to test for unimodality while fitting just a generalized linear mixed model without any squared or other polynomial term. A GLMM is, of course, a linear model. Despite this fact, it can be used to detect unimodality and to fit unimodal data, with the provision that the differences in niche widthsamongspecies are not too large. As graphical tool we suggested to plot the random site effects against the environmental variable. There is an indication for unimodality, when this graph shows a quadratic relationship. The efficacy of GLMM to analyse unimodal data is illustrated by comparing the GLMM approach with an explicit unimodal model approach on simulated data and real data that show unimodality.
When a system is described by a statistical model, model complexity leads to a very large computing time and poor estimation, especially if the number of predictors is large relative to the data size. As an alternative to and improvement over stepwise methods, shrinkage methods have been proposed. One of these is the Relevance vector machine (RVM). RVM assigns individual precisions to weights of predictors which are then estimated by maximizing the marginal likelihood (Type-II ML or empirical Bayes). We also investigated the selection properties of RVM both analytically and by experiments. We found that RVM is rather tolerant for predictors to stay in the model and concluded that RVM is not a real solution in high-dimensional data problems.
By further study the multi-trait and multi-environmental variablemodel selection method developed that used our previous study in a linear mixed model context. The method is called tiered forward selection. In the first tier, the random factors are selected, in the second, the fixed effects are selected and in the final tier non-significant terms are removed based on a modified Akaike information criterion. The linear mixed model with the tiered forward selection is compared with Type-II ML and existing methods for detecting trait-environment relationships that are not based on mixed models, namely the fourth corner method and the linear trait-environment method (LTE).
Hebben grauwe ganzen een negatief effect op weidevogels?
Kleijn, D. ; Hout, J.J. van der; Jansman, H.A.H. ; Kats, R.J.M. van; Knecht, E. ; Lammertsma, D.R. ; Muskens, G.J.D.M. ; Melman, T.C.P. - \ 2011
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2233) - 50
ganzen - weidevogels - biologische mededinging - interacties - populatiedichtheid - vegetatie - natuurbescherming - anser - nederland - geese - grassland birds - biological competition - interactions - population density - vegetation - nature conservation - netherlands
Dit tussenrapport beschrijft een deel van de werkzaamheden die in het kader van het onderzoeksproject ‘Populatiebeheer overzomerende (grauwe) ganzen’ (BO-02-013-005) in 2009 en 2010 hebben plaatsgevonden. Het aantal ganzen dat in Nederland broedt neemt de laatste decennia spectaculair toe. Onder natuurbeschermers is ongerustheid ontstaan dat ganzen een negatief effect hebben op weidevogels. Daarom worden sinds een aantal jaren in en om natuurreservaten aantal-regulerende maatregelen voor de Grauwe gans genomen. Dit rapport presenteert de resultaten van een studie die tot doel had vast te stellen of er een (negatieve) relatie bestaat tussen het voorkomen van overzomerende Grauwe ganzen en weidevogels. In negen gebieden waar ganzen en weidevogels in substantiële aantallen voorkwamen, is onderzocht of de dichtheid of populatietrends van ganzen en weidevogels met elkaar gerelateerd waren. Daarnaast is geanalyseerd hoe de ruimtelijke verdeling tussen ganzen en weidevogels zich gedurende het broedseizoen ontwikkelde: mijden ze elkaar of komen ze juist samen voor? Daarbij is onderscheid gemaakt tussen directe beïnvloeding (aanwezigheid van ganzen) en indirecte beïnvloeding (via de vegetatie).
Newcomers in plant communities : interactions with soil and climate change
Meisner, A. - \ 2011
Wageningen University. Promotor(en): Wim van der Putten, co-promotor(en): W. de Boer. - [S.l.] : S.n. - ISBN 9789085859826 - 136
plantengemeenschappen - invasieve soorten - stikstofkringloop - planten - klimaatverandering - bodem - geïntroduceerde soorten - stikstof - ecosystemen - interacties - plant communities - invasive species - nitrogen cycle - plants - climatic change - soil - introduced species - nitrogen - ecosystems - interactions
Shrubs in the cold : interactions between vegetation, permafrost and climate in Siberian tundra
Blok, D. - \ 2011
Wageningen University. Promotor(en): Frank Berendse, co-promotor(en): Monique Heijmans; Gabriela Schaepman. - [S.l.] : S.n. - ISBN 9789461730251 - 152
struiken - vegetatie - permafrost - kou - klimaat - interacties - toendra - arctische ecologie - plantenecologie - siberië - shrubs - vegetation - cold - climate - interactions - tundra - arctic ecology - plant ecology - siberia
The Arctic is experiencing strong increases in air temperature during the last decades. High-latitude tundra regions are very responsive to changes in temperature and may cause a shift in tundra vegetation composition towards greater dominance of deciduous shrubs. With increasing deciduous shrub cover, the surface albedo (proportion of sunlight that is reflected to the atmosphere) may be reduced and lead to air warming by trapping more solar radiation into the Arctic ecosystem. As a result of this warming, thawing of carbon-rich permafrost soils may increase and cause a large greenhouse gas flux to the atmosphere, thus contributing to global warming.
In my thesis I studied how climate influences shrub growth in the Siberian tundra and how climate-induced changes in shrub cover affect summer permafrost thaw and surface albedo. I investigated these interactions between climate, permafrost and Arctic shrub growth using a combination of shrub ring width analysis, field experiments and remote sensing techniques. I measured and compared growth ring widths with meteorological station data and observed that shrub growth is stimulated by higher summer air temperatures. By performing a shrub removal experiment, I demonstrated that a temperature-induced increase in shrub cover may reduce summer permafrost thaw. Shading by the shrub canopy reduced the transfer of energy to the soil. A denser shrub cover thus effectively reduces summer permafrost thaw, despite leading at the same time to a lower surface albedo. These results indicate it is important to incorporate feedbacks between shrub growth, climate and permafrost thaw in model predictions on the Arctic climate and stability of permafrost in a future warmer world.
Climate change induced range-expanding plants : aboveground and belowground interactions
Morriën, W.E. - \ 2011
Wageningen University. Promotor(en): Wim van der Putten. - [S.l.] : S.n. - ISBN 9789085859376 - 144
planten - geïntroduceerde soorten - klimaatverandering - bodemfauna - vrijlevende nematoden - bodembacteriën - rizosfeer - plaagresistentie - ziekteresistentie - herbivoren - interacties - plants - introduced species - climatic change - soil fauna - free living nematodes - soil bacteria - rhizosphere - pest resistance - disease resistance - herbivores - interactions
Burning of fossil fuels has raised the level of atmospheric carbon dioxide, which contributes to global climate warming. As a result the mean earth surface temperature has increased faster in the past decades than in the previous thousands of years before. This rapid climate warming together with habitat fragmentation and other land use changes puts a major pressure on many plants and animals. They should either adapt to the warmer climate conditions or disperse in order to keep up with their optimal climatic conditions. Range expansion brings new interactions within the ecosystem in the new range. This can lead to potential benefits, for example range shifting species that do not encounter natural enemies in the new range might become invasive. Although invasive species are a well-studied phenomenon, there is relatively little known about the general mechanisms of biological invasions under climate change. In this thesis I focus on plant species that expand range due to current climate warming. I examined how these range-expanding plants interact with aboveground herbivorous insects and - mostly - how they establish belowground interactions with components of the soil food web. I examined how these interactions in the new range may play a role in the successful establishment of climate change induced range-expanding plants in plant communities of the new range. The focus of my study was on riverine (riparian) areas along the great rivers in the Netherlands, which are well connected with southern Europe by the Rhine and Rhine-Danube canal.
In the first experiment we examined exotic plant exposure to aboveground and belowground enemies. We used plants that originated from Eurasia (intra-continental range expanders) and plants that originated from other continents (inter-continental range expanders). We compared these exotic plants with phylogenetically related natives. We grew the plants with and without non-coevolved polyphagous (generalist) herbivores, a locust Schistocerca gregaria and an aphid Myzus persicae. We also exposed all plants to a general soil community from the invaded range and compared their plant-soil feedback responses. Then I tested how individual plants responded to aboveground and belowground plant enemies and I compared this to their combined effects. I also tested whether the strength of aboveground control by generalist shoot-feeding insects was indicative of the strength of belowground control by plant-soil feedback.
In the next study I examined how the soil nematode community from the new range responds to exotic plant species compared to related native plants species. As a follow up, I determined the rhizosphere community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF) and fusaria. All groups of microbes were analyzed qualitatively and the non-mycorrhizal fungal biomass and fusaria were also analyzed quantitatively. I tested the hypothesis that range-expanding plant species have a different rhizosphere microbial community composition than natives.
Finally, I compared the early establishment of range-expanding exotics and phylogenetically related plant species that are native in the invaded habitats. In a greenhouse I grew five range-expanding plant species and five related natives in sterilized and non-sterile inoculated soils from the new range, both alone and with a background community of plant species present in the invaded habitat. In the field, I grew the same plants species in artificially created sparse and dense plant communities. I tested whether range-expanding exotic plant species establish better under competition with native vegetation than phylogenetically related natives, because exotics may benefit from less negative interactions with the soil community compared to natives.
On the ecology and evolution of microorganisms associated with fungus-growing termites
Visser, A.A. - \ 2011
Wageningen University. Promotor(en): Rolf Hoekstra; Thomas Kuijper, co-promotor(en): Duur Aanen; Fons Debets. - S.l. : s.n. - ISBN 9789085859147 - 175
isoptera - schimmels - evolutie - symbiose - interacties - symbionten - ecologie - fungi - evolution - symbiosis - interactions - symbionts - ecology
Bovengrondse-ondergrondse biodiversiteit: het effect van bodemroofmijten op tabakstrips : verslag trips-roofmijt experiment in 2009
Belder, E. den; Elderson, J. - \ 2010
Wageningen : Plant Research International (Nota / Plant Research International 663) - 18
phaseolus vulgaris - insectenplagen - thrips tabaci - roofmijten - macrocheles - mulchen - bodembescherming - interacties - landbouwkundig onderzoek - methodologie - gewasbescherming - preien - boven- en ondergrondse interacties - insect pests - predatory mites - mulching - soil conservation - interactions - agricultural research - methodology - plant protection - leeks - aboveground belowground interactions
Het doel van dit onderdeel bovengrondse-ondergrondse biodiversiteitsproject is vast te stellen óf en in welke mate er interactie plaats vindt tussen ondergrondse roofmijtenpopulaties en mulchen met stro en de bovengrondse plaag tabakstrips.
The role of non-specific interactions in nuclear organization
Nooijer, S. de - \ 2010
Wageningen University. Promotor(en): Ton Bisseling; Bela Mulder, co-promotor(en): Joan Wellink. - [S.l. : S.n. - ISBN 9789085857921 - 117
arabidopsis - celkernen - chromosomen - genomen - chromatine - interacties - cytogenetica - moleculaire biologie - nuclei - chromosomes - genomes - chromatin - interactions - cytogenetics - molecular biology
The most important organelle in eukaryotic cells is the nucleus. Many processes occurring within the nucleus depend on spatial organization of the nucleus. The spatial organization of the eukaryotic nucleus derives from interactions between its constituents. Both specific interactions, for instance the interactions between a DNA binding protein and its target DNA sequence, and non-specific interactions occur. Non-specific interactions stem from physical encounters between molecules or particles, which can favour particular organizations, i.e. the ones that have the lowest entropy. The role of non-specific interactions in nuclear organization is so far not extensively studied. Here, we investigate the effects of non-specific interactions on nuclear organization, using molecular dynamics simulation techniques. Chromatin folding models can be implemented in these simulations as chains of monomers, which can form loops, branches or networks. Through a comparison of simulation results with experimental data, these models can be verified or falsified.
We used MD simulations of models for Arabidopsis chromatin organisation to show that non-specific interactions can explain the in vivo localisation of nucleoli and chromocenters. Also, we quantitatively demonstrate that chromatin looping contributes to the formation of chromosome territories. Focussing on the forces driving nuclear organization in the rosette model, we derive effective interaction potentials for rosette-loop interactions. These potentials are weak, but nevertheless drive chromocenters and nucleoli to the nuclear periphery and away from each other.
We also study the folding of a single human chromosome within its territory. The results of our simulations are analysed using a virtual confocal microscope algorithm which has the same limitations as a real confocal microscope. Thus we show that chromatin looping increases the volume occupied by a 10Mbp chromosomal sub-domain, but decreases the overlap between two neighbouring sub-domains. Our results furthermore show that the measured amount of overlap is highly dependent on both spatial resolution and signal detection threshold of the confocal microscope, and that in typical fluorescence in situ hybridisation experiments these two factors contribute to a gross underestimation of the real overlap. Zooming out to whole nucleus organization, we show that an interplay between interactions between heterochromatin and nuclear lamina generates a wide variety of nuclear organizations, with those occurring in nature requiring a fine balance between both interactions.
The differences between chromosome folding in human and Arabidopsis can be explained through differences in genomic structure and chromosome loop formation, but the underlying mechanisms and forces that organize the nucleus are very similar. The insight how specific and non-specific forces cooperate to shape nuclear organization, is therefore the most important contribution of this thesis to scientific progress.
Opponents and supporters of water policy change in the Netherlands and Hungary
Werners, S.E. ; Warner, J.F. ; Roth, D. - \ 2010
Water Alternatives 3 (2010)1. - ISSN 1965-0175 - p. 26 - 47.
waterbeleid - verandering - individuen - interacties - communicatie - hongarije - nederland - invloeden - water policy - change - individuals - interactions - communication - hungary - netherlands - influences
This paper looks at the role of individuals and the strategies that they use to bring about or oppose major policy change. Current analysis of the role that individuals or small collectives play in periods of major policy change has focussed on strategies that reinforce change and on the supporters of change. This paper adds the perspective of opponents, and asks whether they use similar strategies as those identified for supporters. Five strategies are explored: developing new ideas, building coalitions to sell ideas, using windows of opportunity, playing multiple venues and orchestrating networks. Using empirical evidence from Dutch and Hungarian water policy change, we discuss whether individuals pursued these strategies to support or oppose major policy change. Our analysis showed the significance of recognition of a new policy concept at an abstract level by responsible government actors, as well as their engagement with a credible regional coalition that can contextualise and advocate the concept regionally. The strategies of supporters were also used by opponents of water policy change. Opposition was inherent to policy change, and whether or not government actors sought to engage with opponents influenced the realisation of water policy change.
Evaluatie Opvangbeleid 2005-2008 overwinterende ganzen en smienten. Deelrapport 10. Hebben overwinterende ganzen invloed op de weidevogelstand?
Kleijn, D. ; Winden, E. van; Goedhart, P.W. ; Teunissen, W. - \ 2009
Wageningen : Alterra (Alterra-rapport 1771) - 43
ganzen - biologische mededinging - interacties - populatiedynamica - ecologische verstoring - overwintering - nederland - weidevogels - geese - biological competition - interactions - population dynamics - ecological disturbance - netherlands - grassland birds
Dit rapport richt zich op de vraag of de sterk toegenomen dichtheden ganzen in bepaalde gebieden mede verantwoordelijk kunnen zijn voor de achteruitgang van de weidevogels ter plekke. Gebruik makend van data verzameld in de periode 1990-2005 in het kader van het weidevogelmeetnet en de watervogeltellingen in ganzentelgebieden werd onderzocht in hoeverre gebieden met hoge dichtheden ganzen overlappen met gebieden met hoge dichtheden weidevogels. De effecten van hoge dichtheden overwinterende ganzen op in Nederland broedende weidevogels lijken verwaarloosbaar of positief. Resultaten van onderzoek van SOVON en Alterra
Modelling habitat preference and estimating the spatial distribution of Australian Sea Lions (Neophoca cinerea); "A first exploration "
Aarts, G.M. ; Brasseur, S.M.J.M. - \ 2008
Texel : IMARES (Report / Wageningen IMARES C107/08) - 18
neophoca cinerea - ruimtelijke verdeling - populatie-ecologie - telemetrie - mitigatie - interacties - visserij - ruimtelijke ecologie - spatial distribution - population ecology - telemetry - mitigation - interactions - fisheries - spatial ecology
Managing the Australian sea lion (Neophoca cinerea) population and mitigating its interactions with commercial fisheries, requires an understanding of their spatial distribution and habitat preference at sea. Numerous wildlife telemetry devices have been attached to individual seals from different colonies, providing a detailed insight into there movement and activities. However, as data are only available from some individuals from 16 of 40 colonies in South Australia, these data represents only a small proportion of the population. Moreover, some colonies are poorly represented. To estimate the spatial distribution of the entire South Australian population, one can first investigate why individuals visit certain places and use this information to predict the spatial distribution for other regions lacking data. In this study we fit Generalized Additive Mixed Models (GAMMs) to wildlife telemetry data collected from adult female Australian sea lions to investigate the species’ habitat preference for the variables distance to the colony, depth and slope. The results show that in general they have a higher preference for shallow areas, places close to the colony and a steep slope, but they also display large individual variability. Preference for these variables does not seem to differ between individuals of different sizes. In some of the most western colonies, some individuals seem to spend more time further away from the colony, but apart from this, there is no apparent effect of the longitudinal capture position on preference. The predicted spatial distribution is largely driven by the distance from the departure colony and the actual distribution of individuals among the different colonies. Although depth and slope does seem to effect their distribution to some extent, the most important variables that explain fine-scale foraging activities at-sea are probably missing. Future studies using GPS transmitters attached to animals, that yield high resolution locations and more detailed environmental data, in combination with the analytical technique presented here, should provide more insight there foraging decisions. This should eventually also improve the spatial prediction of the population as a whole.
Plants on the move: plant-soil interactions in poleward shifting plant species
Grunsven, R.H.A. van - \ 2008
Wageningen University. Promotor(en): Frank Berendse; Wim van der Putten, co-promotor(en): Elmar Veenendaal. - [S.l.] : S.n. - ISBN 9789085852513 - 140
planten - plantenecologie - plantensuccessie - invasies - soorten - bodem - interacties - rizosfeer - bodemflora - bodemfauna - klimaatverandering - bodem-plant relaties - plants - plant ecology - plant succession - invasions - species - soil - interactions - rhizosphere - soil flora - soil fauna - climatic change - soil plant relationships
As a result of recent global climate change, areas that have previously been climatically unsuitable for species have now become suitable new habitats. Many plant-species are expanding their range polewards, colonizing these newly available areas. If these species are able to expand their range faster than their natural enemies they can become released from these limiting factors. A similar mechanism has been reported for invasive plant species, introduced into foreign continent, which are often found to be released from natural enemies.
An example of an invasive plant species that is introduced into a foreing contintinent is Carpobrotus edulis. This species was found to be negatively affected by the soil community collected in the native range, while the soil communities from the invaded range did not have an effect on plant performance compared to a sterilized control. I hypothesized that a similar reduction of the negative effects of the soil community can occur when plant species shift their range. This hypothesis was tested in a greenhouse experiment. I compared plant-soil feedbacks of three plant species that have recently expanded their range into The Netherlands, with three related native species. The non-native species experienced a significantly less negative effect of plant-soil feedback than the native plant species.
Concurrently with these range shifts local climate is changing and this might affect plant-soil feedback as well. In order to test this plant-soil feedbacks of six range expanding and six related native species were compared at two temperatures, 20°C and 25°C daytime temperature. While again native species showed a more negative plant-soil feedback than the non-native species, temperature did not affect the strength or direction of plant-soil feedback.
Besides pair wise comparisons between native and non-native species in the invaded range, comparisons between the native and non-native range of a range expanding plant can be used to test for effects of range shifts on plant-soil interactions. Rhizosphere soil was collected from populations of Tragopogon dubius in both the native and the recently colonized range. The soil communities from the native range had a more negative effect on plant performance than the soil communities from the invaded range as compared to sterilized controls. T. pratensis, which is native to the entire studied range, did not show this pattern.
As plant-soil interactions are the net effect of many positive and negative factors the less negative effect of plant-soil feedback can be either a result of more positive or less negative effects of the soil community. One of the mutualistic groups of organisms, the arbuscular mycorrhizal fungi (AMF) are known to be a major factor contributing to ecosystem functioning and to the maintenance of plant biodiversity and the most important soil-borne mutualists for many plants. I therefore focus on this group of soil organisms. I compared the association of T.dubius with AMF in the new part of its range with T. pratensis native to this area. Three measures for plant-fungal affinity were compared between these two plant species; the density of AMF propagules able to colonize the plant, the percentage of root length colonized by arbuscular mycorrhiza, and the composition of the resulting AMF community in the roots. This was done for four replicate soil inocula from different sites in The Netherlands. The two plant species did not differ in any of the tested factors. As there are no differences in the association with the most important mutualist the observed differences in plant-soil interaction are likely an effect of release from negative components in the soil community, e.g. soil pathogens, but further studies are needed to test this.
Alterations in biotic interactions, through climate change and range shifts, such as a release of soil-borne natural enemies, can have significant effects on the performance of plants. Predictions of future ranges and impact of range expanding plant species on invaded ecosystems can therefore not be accurately made without a thorough understanding of its biotic interactions and the way these interactions are changed by the range shifts.
A differential role for corticosteroid receptors in neuroendocrine-immune interactions in carp (Cyprinus carpio L.)
Stolte, H.H. - \ 2008
Wageningen University. Promotor(en): Huub Savelkoul; G. Flik, co-promotor(en): Lidy van Kemenade. - [S.l.] : S.n. - ISBN 9789085851998 - 231
karper - corticoïden - hormoonreceptoren - immunologie - immuniteit - immuniteitsreactie - interacties - stress - cytokinen - visteelt - neuroendocrinologie - carp - corticoids - hormone receptors - immunology - immunity - immune response - interactions - cytokines - fish culture - neuroendocrinology
In this thesis we investigated the involvement of the receptors for the stress hormone cortisol in stress and immune regulation. We set out to characterise the pro-inflammatory cytokine interferon gamma (IFN-γ). Furthermore, we used a genome wide screen (microarray) to search for additional genes that might be involved in regulation of the stress or the immune response.
In teleostean fishes cortisol can be bound by different receptors encoded by at least three different genes. An ancestral corticosteroid receptor (AncCR) is assumed to have been an effective receptor for cortisol in the ancestors of fishes. An early genomic duplication in the fish lineage, over 450 million years ago, led to separate glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) genes, both of which retained the ability to bind cortisol. A second major genomic duplication event took place only in teleostean fishes (not in other vertebrates), and gave rise to duplicate GR genes (GR1 and GR2). Even more variants developed as a result of alternative splicing of the GR1 gene which introduces a nine amino acid insert in the DNA-binding domain of GR1a, GR1b does not have this insert.
To investigate how one ligand can regulate many and very diverse functions using multiple receptors, we describe the expression of GR1 (a and b), GR2 and MR and their sensitivity for cortisol in chapters 3 and 4. The three receptors are expressed in tissues that make up the neuroendocrine stress-axis (brain, hypothalamus and pituitary) and in cells that produce corticotropin-releasing hormone (CRH) and adrenocorticotropic hormone (ACTH). Decreased mRNA expression in brain after prolonged stress suggests an involvement in regulation of hypothalamo-pituitary-interrenal (HPI)-axis activity. In cells of the immune system MR expression is very low compared to GR expression and GR2 is preferentially expressed in lymphocytes. Transactivation assays shows that GR1 is a relatively ‘insensitive’ or ‘stress’ receptor, which can only become activated at stress levels of, whereas GR2 is a ‘sensitive’ receptor that will already be activated at basal levels of cortisol such as occur in non-stressed fish. MR sensitivity for cortisol is intermediate. We predict by tertiary protein modelling and confirmed by transfection assays, that the transactivation capacity of both splice variants (GR1a and GR1b) is similar. Based on the very low expression level in immune cells and the moderate transactivation capacity of MR we concluded that GRs rather then the MR primarily convey stress signals to the immune system. Next, we determined the expression profile of the duplicated GR genes in the immune system in chapters 4 and 5 to investigate the regulation of stress-induced immune modulation. Simultaneously we investigated the expression profile of (among others) heat shock protein 70 (Hsp70). This protein is required for binding of cortisol to the GR, but also has intrinsic immune modulatory functions, as it was shown to downregulate LPS-induced pro-inflammatory cytokine expression in vitro and in vivo. In head kidney phagocytes we found that only physiological stress levels of cortisol could reduce LPS-induced expression of pro-inflammatory cytokines, a response that appears mediated by the ‘stress’ receptor GR1. Moreover, we found that Hsp70 and GR1 (a and b) expression is increased after an immune stimulus in vitro and in vivo, whereas 24 hr restraint stress or 100nM cortisol-treatment hardly increases Hsp70 and GR1 expression levels. This suggests that an immune stimulus rather than increased cortisol levels increases the sensitivity for glucocorticoid regulation and thereby of the cytokine profiles in immune cells.
To find additional genes involved in bidirectional neuroendocrine-immune communication we applied a genome wide screen of 9000 randomly picked cDNA clones. This has the advantage of an unprejudiced overview of regulated genes, but the sensitivity of the technique is limited. In chapter 6 we describe a microarray experiment in which we compared mild acute stress, to prolonged severe immune stimulation. We show that an immune response after parasite infection appears tightly regulated and comparable between individuals, whereas a mild acute stressor allows for more variable gene expression profiles. We found LOC406744 of the DUF727 protein family and nephrosin as new interesting candidate genes that may be involved in neuroendocrine-immune communication.
The key pro-inflammatory cytokine IFN-γ, which is hypothesised to affect neurotransmitter and hormone release, had not been investigated in carp. In chapter 7 we show that carp have duplicate IFN-γ genes that are expressed in immune cells. IFN-γ-2 shows structural and functional characteristics simlar to those in other vertebrate IFN-γ genes and appears to be involved in T-lymphocyte function, whereas IFN-γ-1 is expressed in stimulated B-lymphocytes. Currently recombinant proteins are being produced which will enable us to further elucidate the role of both IFN-γ gene products in the immune system as well as in mediating the neuroendocrine stress response.
Interestingly, as explained in chapter 8, both the glucocorticoid receptor and the IFN-γ genes are duplicated. The duplication-degeneration-complementation (DCC) model has been proposed as an explanation for the high retention of duplicate genes in fishes. The hypothesis assumes that following gene duplication, the two gene copies degenerate over time by random mutation to perform complementary functions that jointly match that of the single ancestral gene, termed ‘subfunctionalisation’. Indeed it appears that the duplicate GR genes have divided the general and ‘stress-related’ functions, reflected by their different sensitivity for cortisol. The duplicate IFN-γ genes appear to have divided B- and T-lymphocyte functions as targets suggested by their gene expression profiles upon selective stimulation.
An important conclusion of this thesis is that duplicated glucocorticoid receptors and heat shock proteins are an integral part of the immune system. Immune stimuli rather than increased cortisol levels control GR and Hsp70 expression in immune cells. The differentially regulated expression of GR genes is at the basis of a balanced pro- and anti-inflammatory
cytokine profile, immune cell viability and thus at the basis of the success of the fishes. This thesis illustrates the importance of extensive and effective bidirectional communication between the neuroendocrine and immune systems, which are at the basis of the successful evolution of the vertebrates.
Gewasbescherming van opkomst tot oogst in de gesloten productie
Janssen, A. ; Maanen, R. van; Messelink, G.J. ; Sabelis, M.W. - \ 2008
Gewasbescherming 39 (2008)Suppl.. - ISSN 0166-6495 - p. 17 - 17.
biologische bestrijding - kassen - voedselwebben - voedselketens - interacties - analytische methoden - risicoschatting - glastuinbouw - agro-ecosystemen - plant-herbivoor relaties - insect-plant relaties - biological control - greenhouses - food webs - food chains - interactions - analytical methods - risk assessment - greenhouse horticulture - agroecosystems - plant-herbivore interactions - insect plant relations
The essence of plants
Bouwmeester, H.J. - \ 2008
Wageningen : Wageningen UR - 24
planten - plantensamenstelling - plantenfysiologie - planteninteractie - interacties - plants - plant composition - plant physiology - plant interaction - interactions
Bladproblemen bij hoge daglichtsom en lage EC - Belichtings- en bemestingsonderzoek verschaft benodigde basiskennis (interview met Nieves García en Mary Warmenhoven)
Arkesteijn, M. ; Garcia Victoria, N. ; Warmenhoven, M.G. - \ 2008
Onder Glas 5 (2008)4. - p. 40 - 41.
kassen - teelt onder bescherming - cultuurmethoden - bromelia's als sierplanten - belichting - lichtsterkte - rassen (planten) - plantenvoeding - interacties - gewaskwaliteit - proeven op proefstations - glastuinbouw - bemesting - groenten - potplanten - greenhouses - protected cultivation - cultural methods - ornamental bromeliads - illumination - light intensity - varieties - plant nutrition - interactions - crop quality - station tests - greenhouse horticulture - fertilizer application - vegetables - pot plants
Bij WUR-Glastuinbouw in Bleiswijk vindt een onderzoek plaats naar de effecten van belichtingsintensiteit en -duur en de interacties met voeding bij drie verschillende bromeliarassen. Eind april 2008 is de teeltproef afgerond. De plantgrootte en plantkwaliteit laten een duidelijke interactie zien tussen voeding, lichtintensiteit en belichtingsduur. De ontwikkeling tijdens de bloei lijkt op dezelfde wijze te reageren als de vegetatieve groei
Onkruiden en insecten
Booij, C.J.H. ; Weide, R.Y. van der - \ 2008
onkruidbestrijding - onkruiden - insecten - interacties - waardplanten - onkruidkunde - weed control - weeds - insects - interactions - host plants - weed science
Onkruiden spelen een belangrijke rol in de ecologie van zowel plaaginsecten als hun natuurlijke vijanden. Daardoor kan onkruidbeheersing zowel positieve als negatieven effecten hebben op insectenplagen. Daarom is een verkenning gedaan naar alle mogelijke interacties tussen onkruiden en insecten
Researching with farmers : a study of KARI participatory research practices in context
Kamau, G. - \ 2007
Wageningen University. Promotor(en): Paul Richards, co-promotor(en): R. Karega; Paul Hebinck; Conny Almekinders. - [S.l.] : S.n. - ISBN 9789085047605 - 248
ontwikkelingsstudies - boeren - landbouwkundig onderzoek - onderzoeksinstituten - onderzoeksprojecten - participatie - interacties - sociale interactie - onderzoekers - onderzoeksbeleid - afrika ten zuiden van de sahara - kenya - participatieve methoden - landbouwvoorlichting - development studies - farmers - agricultural research - research institutes - research projects - participation - interactions - social interaction - research workers - research policy - africa south of sahara - participation methods - agricultural extension
Participatory research was introduced into the Kenyan Agricultural research institute to facilitate a farmer driven research process. The present research analysed the historical and current contexts and practices which could have led to partial achievement of the intended objective. Studies conducted on selected farmer research groups, farmer self organized groups, farmer partnerships and school groups’ provided insights for an enhanced research practice. Analysis of the institute’s history revealed continuities and discontinuities in spatial outlay and mandates, institutional culture and operational policies. The ambivalence in commercial and subsistence focus, diverse collaborators’ and donors’ agenda besides researchers’ disciplinary bias and professional ambitions were shown to influence research implementation Overlooking of farmers’ perspectives was shown to render existent structures like joint planning and evaluation committees mostly symbolic. Farmer flexibility in response to emergent realities was illustrated by the dynamic farmers’ technical and social innovations while harnessing of synergy through mutual interaction was illustrated by partnerships and the school groups’. In conclusion, it is argued that existent structures to enhance mutual interaction ought to be re-juvenated through enabling strategies at various levels. This would enhance utilization of innovations by farmers and incorporation of farmer perspectives by the researchers. Areas proposed for further research include how to create functional partnerships, communities of practice and mechanisms to change researchers’ views of farmers perspectives aimed at a research process with capacity to respond to dynamic contextual changes.
Ondergrondse communicatie: de driehoeksrelatie gastheerplant, parasitaire plant en mycorrhiza-schimmel
Kohlen, W. ; Bouwmeester, H.J. - \ 2007
Gewasbescherming 38 (2007)4. - ISSN 0166-6495 - p. 145 - 149.
detectie - zintuiglijke waarneming - waardplanten - parasitaire planten - striga - mycorrhizaschimmels - scrophulariales - interacties - plantenvoeding - wortels - bodemflora - symbiose - detection - organolepsis - host plants - parasitic plants - mycorrhizal fungi - interactions - plant nutrition - roots - soil flora - symbiosis
De ontdekking van strigolactonen laat zien dat planten op grote schaal ondergronds communiceren. Planten produceren die strigolactonen niet om te communiceren met de parasitaire planten, maar met de mycorrhiza schimmels en mogelijk ook andere voor de plant nuttige organismen. De parasitaire planten hebben een mechanisme ontwikkeld om deze communicatie af te luisteren en te gebruiken in hun eigen voordeel. Om het grote belang van deze stoffen verder te onderzoeken heeft Harro Bouwmeester begin 2006 van NWO een Vici-fellowship ontvangen ter waarde van 1.2 miljoen euro. Met een onderzoeksgroep, waartoe ook auteur Wouter Kohlen behoort, probeert hij de genen in kaart te brengen die zijn betrokken bij de productie van strigolactonen en inzicht te krijgen in hoe ze gereguleerd worden. Ook wil het team weten hoe de strigolactonen worden waargenomen door de parasitaire planten en hoe deze stoffen de interactie tussen de gastheer en beide bezoekers - parasitaire planten en mycorrhiza schimmels - reguleren. De bedoeling is dat het onderzoek niet alleen het begrip zal verbeteren van hoe gastheren communiceren met mycorrhiza schimmels en parasitaire planten, maar ook zal bijdragen aan het verminderen van een reusachtig probleem in Afrika, waar in vele landen Striga de oorzaak is van catastrofale oogstverliezen
Structure-function relationship of the baculovirus envelope fusion protein F
Long, G. - \ 2007
Wageningen University. Promotor(en): Just Vlak. - [S.l.] : S.n. - ISBN 9789085046394 - 150
Baculovirus - Baculoviridae - envelopeiwitten - interacties - infectie - dierenvirussen - celinteracties - envelope proteins - interactions - infection - animal viruses - cell interactions
|Ecologische kwaliteitsdoelstellingen in het Nederlandse natuurbeleid
Turnhout, E. ; Hisschemöller, M. ; Eijsackers, H.J.P. - \ 2006
Beleidswetenschap 20 (2006)3. - ISSN 0921-1934 - p. 15 - 32.
natuurbescherming - dierecologie - overheidsbeleid - interacties - wetenschappelijk onderzoek - nature conservation - animal ecology - government policy - interactions - scientific research
Het Nederlandse natuurbeleid maakt gebruik van wetenschappelijke inzichten bij het beschermen en beheren van natuur. Wetenschap is in het bijzonder betrokken bij de vaststelling van natuurwaarden, ecologische kwaliteit en de effecten van menselijk gebruik. Dit artikel gaat over de interacties tussen wetenschap en beleid bij de ontwikkeling van ecologische kwaliteitsdoelstellingen voor de natuurgebieden de Waddenzee (trilaterale Waddenbeleid) en de Veluwe (ecologische verkenning EVV)
Proceedings of the Frontis Workshop on Chemical Ecology: from Gene to Ecosystem Wageningen, The Netherlands 19-23 March 2005
Dicke, M. ; Takken, W. - \ 2006
Dordrecht : Springer (Wageningen UR Frontis Series 16) - ISBN 1402047835 - 189
chemische ecologie - ecologie - ecosystemen - populaties - genen - soorten - gemeenschapsecologie - planten - dieren - interacties - communicatie - insecten - insectenplagen - verdedigingsmechanismen - insect-plant relaties - chemical ecology - ecology - ecosystems - populations - genes - species - community ecology - plants - insects - insect pests - animals - interactions - communication - defence mechanisms - insect plant relations
Chemical ecology is the ecology of body odour. Every organism uses chemical information in intra- and interspecific interactions. Animals emit chemicals to attract a mate or to prevent a competitor from mating with the partner they just mated with. Plants emit chemicals to recruit other organisms to take care of their sex life or to attract bodyguards to defend them against their enemies. Chemical cues mediate a whole gamut of interactions in plant and animal communities. Chemical cues are used to communicate, but can also be exploited in espionage or eavesdropping. To understand the ecology of chemical signalling in communities one needs to carry out manipulative experiments. Such experiments have been done throughout the last century. However, in recent years the degree of precision with which such experiments can be done has grown tremendously as a result of rapidly increasing knowledge at the molecular-genetic level. This opens exciting new avenues to chemical ecologists. The connection of molecular genetics to community ecology and ecosystem ecology provides novel tools to take up old questions that were often hard to answer
Richtingen voor richtlijnen; interacties tussen Nederland en de Europese Commissie in de implementatie van Europese milieurichtlijnen
Neven, M.G.G. ; Turnhout, E. ; Bogaardt, M.J. ; Kistenkas, F.H. ; Zouwen, M.W. van der - \ 2006
Wageningen : WOT Natuur & Milieu (WOt-rapport 25) - 114
milieubeleid - habitats - luchtkwaliteit - richtlijnen (directives) - regelingen - eu regelingen - nederland - interacties - environmental policy - air quality - directives - regulations - eu regulations - netherlands - interactions
Lidstaten hebben tot op zekere hoogte de ruimte om natuur- en milieurichtlijnen, lidstaatspecifiek te implementeren. Er is dus sprake van zogenaamde beleidsruimte. In onderhavige exploratieve studie is gekeken naar de wijze waarop de inhoudelijke, procedurele en procesmatige beleidsruimte is benut bij de implementatie van de Vogel- en Habitatrichtlijn (VHR), de Nitraatrichtlijn, de Kaderrichtlijn Luchtkwaliteit (KRL) en de Kaderrichtlijn Water (KRW). Op basis van een vergelijkende analyse tussen richtlijnen en reflecties op theorie en empirie over interacties, benuttingstrategieën en uitkomsten is een aantal aanwijzingen voor de Nederlandse overheid op een rij gezet om toekomstige botsingen met de Europese Commissie te kunnen voorkomen. Daarnaast zijn een aantal aanbevelingen voor onderzoek geformuleerd. Trefwoorden: implementatieprocessen, Europees milieubeleid, omgevingsrecht, beleidsruimte, interacties en beïnvloedingsstrategieën, derogatie, handelingsperspectieven, Europese Commissie, Nitraatrichtlijn, Vogel-en Habitatrichtlijn, Kaderrichtlijn water, Kaderrichtlijn luchtkwaliteit
Enzyme-induced aggregation of whey proteins with Bacillus licheniformis protease
Creusot, N.P. - \ 2006
Wageningen University. Promotor(en): Harry Gruppen. - [S.l.] : S.n. - ISBN 9085045010 - 128
wei-eiwit - aggregatie - proteïnasen - peptiden - interacties - bacillus licheniformis - whey protein - aggregation - proteinases - peptides - interactions
Whey proteins are commonly used as ingredient in food. In relation with the gelation properties of whey proteins, this thesis deals with understanding the mechanism of peptide-induced aggregation of whey protein hydrolysates made with Bacillus licheniformis protease (BLP). The results show that BLP breaks down hydrophilic segments in the substrate and, therefore, preserves hydrophobic segments that aggregate once exposed to the solvent. Aggregation during hydrolysis prevented further degradation of the substrate, explaining that aggregating peptides are larger than the non-aggregating ones. Solubility experiments performed on fractionated aggregating peptides showed that peptide co-aggregation is an important factor in the aggregation process. Results also showed that the hydrolysates are able to aggregate added parental protein. The aggregating peptides could form a network in which the presence of both insoluble and partly insoluble peptides was required for the aggregation of intact protein.
Landschap in Natuurbalans 2005: signalen over landschapsdynamiek en ruimtegebruik
Dirkx, G.H.P. ; Agricola, H.J. ; Roos-Klein Lankhorst, J. ; Farjon, J.M.J. - \ 2006
Bilthoven : MNP (Rapport / Milieu- en Natuurplanbureau 408763009/2006) - 65
landschap - landgebruik - stadsontwikkeling - stedelijke gebieden - nederland - interacties - platteland - landscape - land use - urban development - urban areas - rural areas - interactions - netherlands
Voor de Natuurbalans 2005 heeft het Milieu- en Natuurplanbureau analyses verricht van veranderingen in het ruimtegebruik en het effect daarvan op de kwaliteit van het landschap. Verstedelijking speelt daar een belangrijke rol in. Tevens neemt men verstening waar in het landelijk gebied: landbouwbedrijven krijgen een meer industrieel karakter met grote schuren en silo's
Architects of nature: environmental infrastructure and the nature-culture dichotomy
Kreike, E.H.P.M. - \ 2006
Wageningen University. Promotor(en): M. Wessel, co-promotor(en): Freerk Wiersum. - [S.l. ] : S.n. - ISBN 9085044448 - 289
milieu - cultuur - interacties - natuurbescherming - menselijke activiteit - milieubescherming - milieubeheer - theorie - environment - culture - interactions - nature conservation - human activity - environmental protection - environmental management - theory
|Microbiological methods for assessing soil quality
Bloem, J. ; Hopkins, D.W. ; Benedetti, A. - \ 2006
Wallingford (UK) : CABI - ISBN 0851990983 - 307
bodem - micro-organismen - bodembiologie - microbiële flora - microbiologie - methodologie - monitoring - interacties - biodiversiteit - bodemkwaliteit - soil - microorganisms - soil biology - microbial flora - microbiology - methodology - interactions - biodiversity - soil quality
This book provides a selection of microbiological methods that are already applied in regional or national soil quality monitoring programs. It is split into two parts: part one gives an overview of approaches to monitoring, evaluating and managing soil quality. Part two provides a selection of methods, which are described in sufficient detail to use the book as a practical handbook in the laboratory. The methods are described in chapters on soil microbial biomass and numbers, soil microbial activity, soil microbial diversity and community composition, and plant-microbe interactions and soil quality.
Among rodents and rhinos: interplay between small mammals and large herbivores in a South African savanna
Hagenah, N. - \ 2006
Wageningen University. Promotor(en): Herbert Prins; H. Olff. - [S.l.] : S.n. - ISBN 9085044677 - 138
kleine zoogdieren - herbivoren - knaagdieren - rhinoceros - biodiversiteit - interacties - savannen - dierecologie - diergedrag - vegetatie - habitatselectie - brandecologie - zuid-afrika - small mammals - herbivores - rodents - biodiversity - interactions - savannas - animal ecology - animal behaviour - vegetation - habitat selection - fire ecology - south africa
Dissecting host plant manipulation by cyst and root-knot nematodes
Karczmarek, A. - \ 2006
Wageningen University. Promotor(en): Jaap Bakker, co-promotor(en): Aska Goverse; Hans Helder. - Wageningen : Wageningen Universiteit - ISBN 9085044642 - 120
globodera rostochiensis - heterodera schachtii - meloidogyne incognita - plantenparasitaire nematoden - waardplanten - plantengroeiregulatoren - auxinen - interacties - reuzencellen - celbiologie - gastheer parasiet relaties - plant parasitic nematodes - host plants - plant growth regulators - auxins - interactions - giant cells - cellular biology - host parasite relationships