The plant kingdom has evolved an enormous number of chemically diverse metabolites that protect plants from biotic and abiotic stresses. The large number of metabolites in a given plant indicates... Show moreThe plant kingdom has evolved an enormous number of chemically diverse metabolites that protect plants from biotic and abiotic stresses. The large number of metabolites in a given plant indicates interactions between metabolites are very likely. The co-occurrence of plant metabolites comprise a natural background where these metabolites have to function and this is often overlooked or ignored in ecological studies. The main goal of this thesis is to understand the importance of metabolite interactions I used assays with a generalist herbivore to study the interactions between chlorogenic acid (CGA), pyrrolizidine alkaloids (PAs) and fractions from Jacobaea plants. I found that PA free bases, PA N-oxides (the oxidized form of free base) and CGA decreased thrips survival. Although PA free bases and CGA decreased thrips survival, the combination of the two toxins was less toxic than the single toxins. In contrast, the combination of PA N-oxides with CGA enhanced the toxicity against thrips in a synergistic way. Adding PAs to different plant fractions showed that metabolite interactions on thrips survival are common as in all tested combinations we found antagonistic and synergistic effects. Clearly, bioactivity of a metabolite is strongly dependent upon the co-occurrence of metabolites in the plant cell. Show less
In this thesis I studied the functions of the zebrafish orthologs of the human TLR5 and TLR2 genes that were shown to be responsible for recognition of bacterial flagellin and a broad spectrum... Show moreIn this thesis I studied the functions of the zebrafish orthologs of the human TLR5 and TLR2 genes that were shown to be responsible for recognition of bacterial flagellin and a broad spectrum of bacterial cell wall components, respectively. One of the focal points of this thesis is the difference at the transcriptomic level of the downstream pathway of the TLR5 and TLR2 receptors and the roles of TLR signaling in host innate immune responses to infection by Mycobacterium marinum, a close relative to Mycobacterium tuberculosis and a natural pathogen of zebrafish. The new possibilities for analysis of transcriptomes using RNA deep sequencing make it highly attractive to analyze the responses of an entire test animal model at the system biology level. Furthermore, we used genetic knockdown and knockout tools to further analyze the function of TLR5 and TLR2 and downstream signaling partners in innate immunity, infectious disease and insulin resistance. Show less
The interplay between evolution and its role in diversification of Nepenthes binds the studies of this thesis. How evolutionary mechanisms and timing relate to molecular divergence and... Show more The interplay between evolution and its role in diversification of Nepenthes binds the studies of this thesis. How evolutionary mechanisms and timing relate to molecular divergence and phylogenetic signal in the genus Nepenthes were investigated. This in conjunction with distribution modeling and mapping anatomical characters – an approach that led to a broad understanding of why and how best to protect specific geographical areas for conservation of Nepenthes. All work was framed with an interdisciplinary approach, each chapter furthering exploration of the connective ties in how past evolutionary history and its impact on diversity helps us to predict future diversity. Show less
The rate of climate warming in the Arctic nearly doubles warming in the temperate regions. In the arctic tundra, this warming has already altered vegetation, with strong declines in lichens... Show more The rate of climate warming in the Arctic nearly doubles warming in the temperate regions. In the arctic tundra, this warming has already altered vegetation, with strong declines in lichens and mosses and expansion of shrubs. This process called “the greening of the Arctic” has important consequences for the global nutrient cycling and emission of green-house gases to the atmosphere. Even though, plant community dynamics has been monitored in tundra, the effect of climate warming on belowground fungi remained largely unknown, despite the known key roles that fungi play providing the plants with water and nutrients in nutrient-poor arctic soils. This thesis addresses the effect of climate warming on arctic soil fungal communities by DNA-metabarcoding. Climate warming had a strong effect on fungal community composition leading to a strong decline in diversity of lichenized, moss-associated, and ectomycorrhizal fungi. Instead, many species of saprotrophic and parasitic fungi took over. These changes are expected to alter nutrient turnover in tundra soils (including decomposition and CO2 flux) and affect populations of plants and animals (for example, caribous that are feeding on lichenized fungi in winter). Show less
Language is a uniquely human trait. All animals have ways to communicate, but these systems do not bear the same complexity as human language. However, this does not mean that all aspects of human... Show moreLanguage is a uniquely human trait. All animals have ways to communicate, but these systems do not bear the same complexity as human language. However, this does not mean that all aspects of human language are specifically human. By studying the language perception abilities of other species, we can discover which parts of language are shared. It are these parts that might have been at the roots of our language evolution. In this thesis I have studied language and music perception in two bird species, zebra finches and budgerigars. For example, zebra finches can perceive the prosodic (intonation) patterns of human language. The budgerigars can learn to discriminate between different abstract (grammar) patterns and generalize these patterns to new sounds. These and other results give us insight in the cognitive abilities that might have been at the very basis of the evolution of human language. Show less
Mycobacterium tuberculosis, the agent of TB, is one of the deadliest human pathogens, infecting one third of the global population. Establishment of infection by mycobacteria relies on complex... Show moreMycobacterium tuberculosis, the agent of TB, is one of the deadliest human pathogens, infecting one third of the global population. Establishment of infection by mycobacteria relies on complex interactions with host innate immune cells, especially macrophages. Once engulfed by macrophages, mycobacteria “usurp” the host cell machineries to facilitate dissemination and to establish an intracellular niche for survival and replication. To investigate how mycobacteria force the immune cells to support infection, we explored the chemokine pathway, best known for its capability to induce cell migration. To dissect the interplay between immune cells and the pathogen, we modelled human TB using the zebrafish-Mycobacterium marinum natural host-pathogen pair, which is attractive for the excellent optical accessibility of the zebrafish larvae and the possibility to apply genetic tools to impair the chemokine signaling. We show that depletion of either CXCR3 or CXCR4 axes are beneficial to the host. Exploitation of CXCR3 signaling leads to macrophage recruitment and to transcriptional changes in macrophages that make them more permissive for mycobacterial intracellular persistence. Activating CXCR4 signaling triggers instead vascularization of the nascent tuberculous granulomas, which in turn supports expansion of the infection. Therefore, inhibitions of these pathways represent promising host-directed therapeutic avenues to counteract mycobacterial diseases. Show less
The explosive increase in infections by pathogens is a major problem in the clinic today. The theme of this thesis was to find novel antibiotics from actinomycetes. Next-generation... Show more The explosive increase in infections by pathogens is a major problem in the clinic today. The theme of this thesis was to find novel antibiotics from actinomycetes. Next-generation sequencing revealed that the biosynthetic potential of actinomycetes had been grossly underestimated. In this thesis, different antibiotics-eliciting strategies, including microbial cocultivation, streptomycin-resistant mutation, overexpression of pathway-specific activator, variation of culture conditions, were utilized to enforce fluctuations in the production of bioactive compounds in actinomycetes, after which, NMR-based metabolic profiling was used to facilitate uncovering those elicited molecules. This pipeline allowed the discovery of new antibiotics involving various chemical skeletons, such as 7-prenylisatin, methoxylated isocoumarins, endophenazines, and C-glycosylpyranonaphthoquinones. On the other hand, genome-mining methodology enabled the discovery of a group of endophenasides and leucanicidin in Kitasatospora sp. MBT66, whereby the rhamnosylation of both scaffold are executed by a same promiscuous glycosyltransferase. Last but not least, a novel antibiotic termed lugdunomycin with unprecedented chemical scaffold, as well as a number of new angucycline-type antibiotics, were characterized from Streptomyces sp. QL37. The biosynthetic pathway of lugdunomycin was deciphered by genetic knockout and OSMAC (One Strain MAny Compound) strategy. In summary, this thesis explores an interface of genomics and metabolomics to accelerate new antibiotics discovery. Show less
Octocorallia (primarily soft corals and gorgonians) occur in cold-water environments as well as in tropical seas and can form a major component of reef communities. Because of their... Show more Octocorallia (primarily soft corals and gorgonians) occur in cold-water environments as well as in tropical seas and can form a major component of reef communities. Because of their abundance and three-dimensional structure octocorals are an important habitat for symbiotic species such as crustaceans, worms, fishes and molluscs. Among the latter group are snails of the family Ovulidae, obligate associates of octocorals. Ovulid snails have adapted their morphological appearance to avoid predation. They can either be perfectly camouflaged or ambiguously coloured to advertise their toxic properties. It was therefore expected that these morphological adaptations would have an evolutionary background, which would corresponds with that of their octocoral hosts. In this thesis the evolutionary history of the Ovulidae and Octocorallia are examined within and between both taxa by using a multifaceted approach, consisting of (calibrated) phylogenetic and co-evolutionary analyses, taxonomic revisions and coral bioactivity research. The results show that snails and octocorals did not coevolve, but that the evolutionary history between both groups is best described as sequential evolution in which the host affects the symbiont but not vice versa. Show less
Jasmonates (JAs) are crucial plant signaling molecules that regulate defense responses against wounding, insects and necrotrophic pathogens. The biosynthesis of JAs is regulated by a positive... Show moreJasmonates (JAs) are crucial plant signaling molecules that regulate defense responses against wounding, insects and necrotrophic pathogens. The biosynthesis of JAs is regulated by a positive feedback loop. This thesis reveals the transcriptional regulatory mechanism behind this positive feedback loop in Arabidopsis. The studies show that the bHLH-domain transcription factors MYC2, MYC3 and MYC4 positively regulate most JAs biosynthesis genes directly and by controlling the expression of ORA47 gene, encoding a regulator of JAs biosynthesis. Show less
This thesis contributed to a broader understanding of the genetic and physiological mechanisms that regulate developmental plasticity represented by butterfly wing color patterns. We found... Show more This thesis contributed to a broader understanding of the genetic and physiological mechanisms that regulate developmental plasticity represented by butterfly wing color patterns. We found that different groups of cells within the same tissue have sensitivities and patterns of response that are distinct for the external environmental cue and for the internal hormonal signal. We also showed that the spatial compartmentalization of these responses cannot be explained by the spatial or temporal compartmentalization of the hormone receptor protein, and that manipulating pupal ecdysteroid levels is sufficient to mimic in direction and magnitude the shifts in adult reproductive resource allocation. We explored the effect of alleles of large effect on wing pattern on plasticity by characterizing thermal reaction norms for the size of eyespot rings for Bicyclus anynana mutants. Genotypes with alleles affecting eyespot size and color were the most sensitive to variation in developmental temperature. To explore genotype, temperature, and genotypextemperature effects on B. anynana development, we derived artificial selection lines expressing wet or dry-season-like phenotypes and, we characterized thermal reaction norms for a wider range of temperatures. Our results provided evidence for significant GxE effects, and also revealed a possible new color appearing at the most extreme low temperatures. Show less
Metastatic cancer is aggressive and rapidly developing, making it difficult to treat, often leading to mortality. Cancer cells are not isolated, but rather survive and proliferate in complex tumor...Show moreMetastatic cancer is aggressive and rapidly developing, making it difficult to treat, often leading to mortality. Cancer cells are not isolated, but rather survive and proliferate in complex tumor microenvironments. Importantly, tumor cells “educate” immune cells to play a supportive role during cancer progression. Therefore, understanding how cancer cells and immune cells communicate is of pivotal importance to limit tumor progression. In this project, we identified the chemokine receptor CXCR4 and its correspondent ligand, CXCL12, as a key couple that regulate the interaction between tumor cells and immune cells. The research has been performed using the zebrafish xenograft model. This model offers the advantage of looking at tumor-immune cell interaction on a single cell level and in a living whole organism. The transparency of the embryo and the current genetic tools available, in combination with the ease in pharmacological approaches, make this model an excellent tool to determine and impair cancer-microenvironment inter-communication. We showed that inhibiting the CXCL12-CXCR4 axis either on the tumor side or on the immune cell side leads to impaired tumor progression, during the early phases of metastasis formation. We propose that blocking cancer-stroma communication represents a promising therapeutic strategy to fight cancer.Show less
Underwater sound is a critical tool for aquatic animals that communicate acoustically or exploit environmental sounds to find prey,avoid predators,for orientation.The interference of... Show more Underwater sound is a critical tool for aquatic animals that communicate acoustically or exploit environmental sounds to find prey,avoid predators,for orientation.The interference of various anthopogenic and natural sound sources can make it difficult to distinguish biologically relevant sounds and can even cause physical damage to these animals.This has given rise to international concern about possible effects of anthropogenic sound sources on marine life due to increasing shipping traffic,exploitation of oil and gas reserves and the development of new offshore energy sources.In this thesis, the spatial, temporal and spectral distributions of sound generated by anthropogenic and natural sources in the Dutch North Sea are investigated. In order to achieve this aim, the acoustic propagation algorithms are developed;compared with other propagation methods;source characteristics are modelled;and the resulting sound distribution is mapped for each source type.The acoustic insights and mathematical tool box that came out should help policy makers, legislators, biologists and conservationists and may serve in ecological monitoring and impact assessments, guide marine research efforts and may be used to determine potential regions or periods of acoustic conflict between human activities and aquatic life. Show less
Fish live in a world that is not silent. In fact, fish hear low frequency sounds and may need them for navigation, predator-prey interactions and mate attraction. Due to their dependence on sounds... Show moreFish live in a world that is not silent. In fact, fish hear low frequency sounds and may need them for navigation, predator-prey interactions and mate attraction. Due to their dependence on sounds, fish may be particularly sensitive to changes in their acoustic world. Since the 1900s, the acoustic world of fish has been altered by a new prominent sound source: human activities. These activities generate a cacophony of high-intensity sounds. At close range, they may cause tissue damage and temporary hearing loss. At further distances, more moderate sounds may cause auditory masking, behavioural changes and reduced efficacy in foraging and avoiding predators. Assessing the severity of behavioural impacts of sounds is not straightforward and are often problematic.This thesis used European seabass to study behavioural effects of man-made sounds of different temporal structures. It also compared the effects of tank-based experiments with open-water experiments. Finally, this thesis studied the habituation of fish to sound exposure and how sound effects are influenced by various environmental factors. Show less
Soil biodiversity is huge and determines largely the functioning of terrestrial ecosystems both at the ‘macro’ and the ‘micro’ level. Despite the general acceptance of the large impact of land use... Show moreSoil biodiversity is huge and determines largely the functioning of terrestrial ecosystems both at the ‘macro’ and the ‘micro’ level. Despite the general acceptance of the large impact of land use and other human activities on species loss in terrestrial ecosystems, their effects on microbial species reduction and the consequences are largely unknown. A major reason is the scarcity of experimental approaches to assess the relevance of soil microbial diversity for the functioning of soil ecosystems. The main goal of the study described in this thesis was to obtain better understanding of the diversity, structuring and functioning of bacterial communities in soil and and rhizosphere. With that purpose, we initially applied the rather old dilution approach to manipulate the diversity of microbial communities in soil by inoculation and subsequent incubation of more or less diluted soil suspensions in pre-sterilized soils. Show less
The Gram-negative soil bacterium Agrobacterium tumefaciens is capable of infecting a large number of dicotyledonous plants, causing crown gall disease. During infection, a small DNA segment (T-DNA... Show moreThe Gram-negative soil bacterium Agrobacterium tumefaciens is capable of infecting a large number of dicotyledonous plants, causing crown gall disease. During infection, a small DNA segment (T-DNA) from the tumor-inducing (Ti) plasmid of the bacterium is delivered via a VirB/D4 Type Four Secretion System (TFSS) into plant cells where it is integrated into the genome. The expression of genes on the T-DNA in transformed plant cells leads to uncontrolled cell division, and ultimately triggers plant tumor formation. Agrobacterium also transfers several virulence (vir) proteins (VirD2, VirD3, VirD5, VirE2, VirE3 and VirF) encoded by genes present in the vir region of the Ti plasmid to host cells via the same TFSS apparatus independently of the T-DNA. In this thesis, I mainly focused on the biological functions of one of these translocated virulence proteins called VirD5. Show less
Over the past few decades, public attention, activities in the field of conservation and animal welfare by nongovernmental organizations (NGOs), and scientific exploration are raising awareness on... Show moreOver the past few decades, public attention, activities in the field of conservation and animal welfare by nongovernmental organizations (NGOs), and scientific exploration are raising awareness on the potential effects of sounds on marine mammals and fish species. The aim of this thesis was to explore sound-induced behavioral changes in fish using captive zebrafish as a model species. I explored behavioural parameters as potential indicators of sound-related stress, disturbance and deterrence. In four different studies, I examined various sound exposure treatments to provide insights that may be useful for future explorations for indoor and outdoor sound impact studies as well as for assessing animal welfare and productivity in captive situations. Furthermore, my findings may also raise awareness for sound levels in laboratories and the potential effect on reliability for fish as a model species for medical and pharmaceutical studies. I also explored the complexity of sound fields in indoor fish tanks by selecting a different set-up for each study, which makes behavioural analyses and direct comparisons not only relevant within each study, but also provides insight into the role of fish tank acoustics on 'natural' and experimental exposure condition. Show less
In the last decades, average land surface temperatures in the Arctic have increased at rates up to six times higher than the global average increase. Similarly, precipitation in the Arctic also... Show moreIn the last decades, average land surface temperatures in the Arctic have increased at rates up to six times higher than the global average increase. Similarly, precipitation in the Arctic also increased, especially during the cold season when most precipitation falls as snow. In this thesis, the long-term effects of summer increased temperatures and increased winter snow depth in arctic soil fungal community composition in dry heath and moist tussock tundra were addressed using long-term ecological experiments at Toolik Lake, Alaska. Soil fungal composition was assessed through soil DNA extraction and massive parallel sequencing of rDNA ITS2. The fungal community composition responded strongly to summer warming in the moist tundra, but not in the dry tundra. Although total fungal richness was not significantly affected by warming, there were clear correlations among richness of various ecological and taxonomic groups and long-term warming. Regarding the effects of increased winter snow depth, the ectomycorrhizal fungal community composition of the dry tundra had a stronger response than the moist tundra community. The observed changes will likely affect ecosystem functions, such as C storage and N turnover, and have the potential to feedback to climate changes. Show less
Photosynthesis is the process that harvests energy from light, and fixes it as chemical energy. It is performed by cyanobacteria, algae, and plants. The overall solar energy to biomass conversion... Show morePhotosynthesis is the process that harvests energy from light, and fixes it as chemical energy. It is performed by cyanobacteria, algae, and plants. The overall solar energy to biomass conversion efficiency of plant photosynthesis is widely considered to be very low. Recent models have indicated that the human demand for plant biomass will exceed the current production capacity in the near future. Improving the efficiency of photosynthesis has since been designated as one of the primary targets for improving crop yield. In order to acquire novel insights into the process of engineering more efficient photosynthesis I have investigated the use of zinc finger artificial transcription factor (ZF-ATF) mediated genome interrogation as a novel tool for the enhancement of photosynthesis-related traits, the results of which are described in this thesis. Show less
In this thesis, we identify and/or analyse a couple of regulators of the TGF-β and Wnt signal transduction pathways that play important roles in breast cancer. Our aim was to understand how these... Show moreIn this thesis, we identify and/or analyse a couple of regulators of the TGF-β and Wnt signal transduction pathways that play important roles in breast cancer. Our aim was to understand how these regulators affect the different steps of these pathways, including receptor activation, post-translational modification of other transducing molecules, target gene transcription, as well as crosstalk with other cell signaling pathways. Insight in these mechanisms is expected to help to design strategies for therapeutic intervention in TGF-β and Wnt mediated breast cancer progression. Show less
The filamentous soil bacteria of the genus Streptomyces are commercially exploited for the production of a wide range of natural products such as antibiotics, anticancer agents and... Show moreThe filamentous soil bacteria of the genus Streptomyces are commercially exploited for the production of a wide range of natural products such as antibiotics, anticancer agents and immunosuppressants. Additionally, there is a strong interest in the use of these bacteria for the production of industrial proteins. Optimal production of these secondary metabolites and enzymes is tightly coupled to morphology. However, relatively little is known about the genetic determinants influencing the morphology of streptomycetes in liquid-grown cultures. The work presented in this thesis focuses on the formation of extracellular macromolecules and their influence on morphogenesis, with a special emphasis on the role of the cellulose synthase-like protein CslA and the radical copper oxidase GlxA in the production of a tip-localized glycan. This research is of fundamental importance for understanding the determinants of growth and development of this multicellular model organism, and at the same time may help us to further optimize their exploitation for the industrial production of secondary metabolites and enzymes. Show less
