The function of TLRs in innate immunity has aroused worldwide attention soon after its discovery. Because of the broad functions of TLR2 in innate immunity, the drive for the development of TLR2... Show moreThe function of TLRs in innate immunity has aroused worldwide attention soon after its discovery. Because of the broad functions of TLR2 in innate immunity, the drive for the development of TLR2-targeted vaccines or therapeutic treatments has accelerated in the last decades. However, its dual role in both activation and suppression of innate immune responses makes it very difficult to use the available results from basic research for the development of clinical trials. In addition, it is still not clear what is the function of TLR2 in regulating phagocytic cell migration. Therefore, we aimed to determine the function of TLR2 in mycobacterial infection and explore its role in regulating phagocytic cell migration in inflammatory tissue by using a zebrafish larval model in this thesis. We showed that infection of a tlr2 mutant in zebrafish larvae leads to a higher mycobacterial burden, accompanied by a lower number of granulomas and increased extracellular bacterial growth. Through a tail fin wounding and tail fin infection zebrafish model, we demonstrated that tlr2 is involved in modulating leukocyte migration. This thesis provides a better understanding of the functions of TLR2 in innate immune responses to infection and tissue wounding. Show less
In this thesis, I study 1) metabolic alterations in tuberculosis related to wasting syndrome in human patients as well as in rodent and fish animal models. 2) effects of the mutation of the leptin... Show moreIn this thesis, I study 1) metabolic alterations in tuberculosis related to wasting syndrome in human patients as well as in rodent and fish animal models. 2) effects of the mutation of the leptin gene on cachexia and diabetes in rodent and zebrafish animal models. 3) how tuberculosis infection and resulting metabolic reprogramming are dependent on leptin signaling in mice and zebrafish larvae. Show less
This thesis describes the antimicrobial discovery strategy developed in our group, the den Hertog Group at the Hubrecht Institute. It includes a cultivation-based screening approach for novel... Show moreThis thesis describes the antimicrobial discovery strategy developed in our group, the den Hertog Group at the Hubrecht Institute. It includes a cultivation-based screening approach for novel antimicrobial agents from the source of fungi, and a bacterial time-lapse imaging approach for antimicrobial mechanism of action (MoA) identification. With this strategy, we have discovered several interesting antimicrobial agents and have demonstrated the detailed antimicrobial property of two of them, berkchaetoazaphilone B (BAB) and harzianic acid (HA). Show less
NNMT wordt beschouwd als een nieuw potentieel farmacologisch doelwit in de behandeling van een verscheidenheid van kankers, stofwisselingsziekten en andere pathologieën. Het toenemend aantal... Show moreNNMT wordt beschouwd als een nieuw potentieel farmacologisch doelwit in de behandeling van een verscheidenheid van kankers, stofwisselingsziekten en andere pathologieën. Het toenemend aantal publicaties waarin de rol van NNMT bij ziekten wordt opgehelderd, heeft op zijn beurt de ontwikkeling van krachtige en selectieve remmers van NNMT gestimuleerd, waarbij in de afgelopen vijf jaar een toenemend aantal verbindingen is onthuld. Hoofdstuk 1 geeft een uitgebreid overzicht van de huidige status van de ontwikkeling van NNMT remmers, relevante in vitro en in vivo studies, en een bespreking van de uitdagingen waar men bij de ontwikkeling van NNMT remmers voor staat. In hoofdstuk 2 werd een gevarieerde bibliotheek van remmers geprepareerd om de verschillende gebieden van de NNMT bindingsplaats te onderzoeken. In hoofdstuk 3 wordt verslag gedaan van een scaffold-hopping strategie om nieuwe en krachtige bisubstraat NNMT remmers te genereren. In hoofdstuk 4 wordt een prodrug strategie beschreven om de polariteit van verbinding 17u te verlagen en de cellulaire activiteit te verbeteren. In hoofdstuk 5 wordt het ontwerp en de synthese beschreven van een bibliotheek van verbindingen die zich richten op de covalente interactie met actieve site cysteïne en serine residuen met behulp van verschillende functionele groepen. Show less
In this thesis, two potential therapeutic targets for diabetic nephropathy were dentified and investigated. First, we show that glomerular clusterin is upregulated in diabetic nephropathy and... Show moreIn this thesis, two potential therapeutic targets for diabetic nephropathy were dentified and investigated. First, we show that glomerular clusterin is upregulated in diabetic nephropathy and demonstrated that recombinant clusterin protein can protect the podocytes against oxidative stress in vitro. Second, we reveal that hCN1 overexpression accelerated and aggravated diabetic nephropathy in BTBR ob/ob mice. We also studied two novel zebrafish models to investigate chronic kidney disease. We showed that lepb-/- adult zebrafish have the early signs of human diabetic nephropathy, and we demonstrated that ctns mutant adult zebrafish have the kidney pathologic features of human nephropathic cystinosis. Show less
Anthropogenic noise has been shown to affect marine animals in various ways, this may have fitness consequences at individual and population level. This thesis aims to increase insight into the... Show moreAnthropogenic noise has been shown to affect marine animals in various ways, this may have fitness consequences at individual and population level. This thesis aims to increase insight into the quantification of sound-induced behavioural responses that are relevant to fitness, and into factors that modulate the responses. I addressed both knowledge gaps using captive and field studies on marine animals from multiple trophic levels. For the quantification of behavioural responses relevant to fitness, I examined the changes in time budgets of Atlantic cod in a net pen and basin in response to sound (chapter 2 and 3). To increase insight into factors that modulate sound impact, I examined the effect of various acoustic characteristics of sound stimuli and the environment on European seabass (chapter 4), the interaction between foraging shore crabs and common shrimps during noise (chapter 6), the cross-sensory interference by noise in foraging crabs (chapter 7), and habituation to repeated sound exposures by blue mussels (chapter 8). Future studies are needed to be able to link changes in time budgets to changes in energy budgets, and consequently to fitness. Additionally, studies into the factors that modulate the effects of sound are needed to fully understand the impact of sound. Show less
Anthropogenic noise negatively affects wildlife in a wide range of taxonomic groups. Especially for birds, a substantial number of observational studies have now shown negative associations between... Show moreAnthropogenic noise negatively affects wildlife in a wide range of taxonomic groups. Especially for birds, a substantial number of observational studies have now shown negative associations between noise pollution and abundance and diversity along roadsides. Researchers investigating birds’ behavioural responses to high level noise to date have mostly focused on the immediate adjustment of vocal signalling behaviour. However, there is more than one mechanism by which birds might cope with increasing noise levels. They may show immediate behavioural reactions, such as spatial avoidance and/or vocal adjustment, but also more ontogenetic adjustments with long-term consequences like changes in sensory and personality traits. To test these potential effects of traffic noise on birds, I conducted a series of experiments using zebra finches. I have demonstrated that traffic noise per se can contribute to spatial avoidance in birds and cause variation in parental behaviour, and that there can be changes in noise avoidance behaviour in the course of a lifetime. These results provide new insights into the potential impacts of noise on birds. Show less
Soil is a home for an unbelievable diversity and abundance of microbial life that is essential for supporting life on our planet. Microorganisms living in soil take part in cleaning our water,... Show moreSoil is a home for an unbelievable diversity and abundance of microbial life that is essential for supporting life on our planet. Microorganisms living in soil take part in cleaning our water, degrading toxic compounds and recycling nutrients, and last but not least, they are essential partners to plants. Through their roots, plants release a mix of secretions to attract microorganisms, creating a remarkable environment called the rhizosphere. The rhizosphere is populated by microbes who often provide beneficial services to plants, like nutrient acquisition, growth promotion and protection against diseases. Modern agriculture suffers from losses caused by crop diseases, and a common way of controlling diseases is using pesticides. Pesticides often have a negative impact on the environment, and disease-causing agents (pathogens), can become resistant with time. One of the possible solutions to this problem is based on soil microbial communities. Due to the activity of their microbiome, some soils possess a natural capacity to protect plants against diseases. These soils are called disease suppressive soils, and the investigation of the microbial mechanisms leading to the natural protection of crops is the topic of this thesis. In our work we used a common pathogen of cereals, fungus Fusarium culmorum, and wheat, to first, identify suppressive soils able to protect this plant from the pathogen, and, investigate the mechanisms of protection using e.g. sequencing and mass spectrometry. During our project we identified potential microbes, genes and metabolites involved in soil disease suppressiveness. Moreover, we evaluated the impact of microplastic on the soil disease suppressiveness. Show less
Autopaghy is an intracellular degradation system which targets cytosolic components to lytic compartments for degradation and recycling of the building blocks of the cell. The process is highly... Show moreAutopaghy is an intracellular degradation system which targets cytosolic components to lytic compartments for degradation and recycling of the building blocks of the cell. The process is highly induced by carbon starvation conditions. In this thesis, different roles of autophagy in the filamentous fungus Aspergillus niger were studied, focusing on its role during carbon starvation, endoplasmic reticulum (ER) stress and unconventional protein secretion. Show less
The ongoing increase in antimicrobial resistance combined with the low discovery of novel antibiotics is a serious threat to our health care. Genome mining has given new potential to the field of... Show moreThe ongoing increase in antimicrobial resistance combined with the low discovery of novel antibiotics is a serious threat to our health care. Genome mining has given new potential to the field of natural product discovery, as thousands of biosynthetic gene clusters (BGCs) are discovered for which the natural product is not known.Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a highly diverse class of natural products. The large number of different modifications that can be applied to a RiPP results in a large variety of chemical structures, but also stems from a large genetic variety in BGCs. As a result, no single method can effectively mine for all RiPP BGCs, making it an interesting source for new molecules.In this thesis, new methods are explored to mine genomes for the BGCs of novel RiPP variants, with a focus on discovering RiPPs that have new modifications. RRE-Finder is a new tool for the detection of RiPP Recognition Elements, domains that are often found in RiPP BGCs. DecRiPPter is another tool that employs machine learning models to discover new RiPP precursor genes encoded in the genomes. Both tools can be used to prioritize novel RiPP BGCs. Two candidate BGCs are characterized, one of which could be shown to specify a new RiPP, validating the approach. Show less
The soil ecosystem consists of the largest reservoir of biodiversity on Earth. Microbial communities are unseen drivers in soil ecosystems and they play an important role in determining a wide... Show moreThe soil ecosystem consists of the largest reservoir of biodiversity on Earth. Microbial communities are unseen drivers in soil ecosystems and they play an important role in determining a wide variety of soil processes in terrestrial ecosystems. Soil microbial communities can influence plant performance and can drive plant species composition on a particular soil. Soil microbes are associated with an extensive range of ecosystem processes, in turn, affect plant growth. While these processes can benefit plant growth, the soil microbial community also harbors microbes that compete with plants for nutrients or are pathogenic and impair plant growth. This leads to the question if plants can manipulate the composition of the soil microbial community to their advantage.In agriculture, the physical structure of the soil is often altered to improve crop production and this modifies biological components and microbial properties of the soil. Moreover, green crop management technologies, such as regulation of soil microbial biodiversity, application of beneficial microbial agents and induction of plant hormonal resistance, are regarded as promising approaches against pests and microbial pathogens. Although many experiments have shown that activation of hormonal signaling pathways can boost a plant’s immunity against pathogenic microbial attacks, whether and how these hormonal signaling pathways affect the soil microbial community and consequently plant growth is still poorly understood. Therefore, to better understand the roles of soil microbial communities at both taxonomic and functional level, studies from a plant defensive perspective are timely and needed, and this is the main focus of this thesis. Show less
Marine sponges are important members of reef ecosystems, as they play ecological roles that are essential for the health of the reef. From a chemical perspective, sponges have been widely studied,... Show moreMarine sponges are important members of reef ecosystems, as they play ecological roles that are essential for the health of the reef. From a chemical perspective, sponges have been widely studied, showing great chemical diversity with biological activity, although this chemical diversity can often not be linked to for instance variation in environmental conditions experienced by sponges. Metabolomics, with its holistic overview of the metabolites present in samples, has provided new tools to gain insight into the function of metabolites in the intricate relationship between sponges and their environment. Among sponges, giant barrel sponges have stood out for their predominance in many reefs, their longevity and the fact that they are widely spread across oceans. this thesis showed how environmental, genetic and biological factors individually or as a result of their interaction can influence the metabolome of giant barrel sponges. This is only the first step towards a better understanding of the role that chemical compounds play in interactions between sponges and the surrounding environment. The advances in this field will rely, among others, on the development of technologies that would allow real time measurement of the metabolome and the study of the interaction between the metabolome and other omics. Show less
Taxonomy as a science has accumulated data and knowledge for more than 250 years. The quality and usefulness of the facts recorded in taxonomic literature has greatly improved from the early... Show moreTaxonomy as a science has accumulated data and knowledge for more than 250 years. The quality and usefulness of the facts recorded in taxonomic literature has greatly improved from the early descriptive texts to the modern data-rich, hypothesis-driven works. Our work illustrates the application of some of the “e-taxonomic” tools and the “New Taxonomy” thinking explored in the introduction. Here, we analyzed specimen data contained in legacy taxonomic literature in Chapters 2 and 3—to observe species distribution of one spider group and genital evolution, respectively—and also explored an integrative perspective that involves describing new taxa and testing phylogenetic hypotheses using molecular and morphological data, as done in Chapter 4 and 5. Show less
Freshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species. European and national regulation... Show moreFreshwater is an important resource, but at a great risk of species decline due to habitat loss, pollution and over-exploitation, and invasive alien species. European and national regulation dictate the monitoring of freshwater quality in the Water Framework Directive. The biological elements of these assessments focus on the organisms living in freshwater systems, such as fish, macroinvertebrates, and plants. Traditional monitoring of quality relies on labor-intensive and expensive collection and morphological identification of specimens. Recent developments in molecular techniques allow for easier identification through (meta)barcoding and species detection using environmental DNA (eDNA). This thesis explores the possibilities to integrate genetic tools into freshwater quality monitoring and impact assessments, by investigating the ability of DNA-based methods to approximate morphologically determined species occurrences and the influence of their abundance on quality ratios. Additionally, it examines the effects of replication strategies in eDNA sampling, and studies the implications of using eDNA monitoring across several trophic levels of the ecosystem in impact assessments. Combined with a growing body of literature, the findings in this thesis illustrate that molecular techniques will contribute to a better ecosystem understanding and allow for more effective monitoring and management of freshwater systems, safeguarding the ecosystem services provided to humankind. Show less
This thesis presents the systematics, epidermal defense, and bioprospecting of wild orchids. I mainly targeted Indonesian orchids, with particular emphasis on the genus Glomera with 169 species.... Show moreThis thesis presents the systematics, epidermal defense, and bioprospecting of wild orchids. I mainly targeted Indonesian orchids, with particular emphasis on the genus Glomera with 169 species. Four main challenges of this group of orchids were tackled. First of all, a web-based multilingual interactive key of Glomera, one of the lesser-known genera in the horticulturally popular necklace orchids, was constructed. This key simplifies species identification for further taxonomic revisions by both specialists and amateur orchid enthusiasts. Secondly, identification of non-flowering Glomera specimens in botanical gardens was sped up by producing DNA barcodes of herbarium preserved flowering type specimens. These DNA barcodes were matched with data obtained from vegetative fresh plants. Thirdly, improving protection of orchids in botanic gardens and nature reserves against herbivory was investigated. Centrifuge and feeding experiments showed that leaf trichomes and wax layers reduce both the adhesion and appetite of herbivorous snails. Lastly, bioprospecting was explored to help financing the maintenance of orchid collections in botanical gardens and protection of nature reserves. For this, traditional medicinal use was compiled from the literature and plotted on a molecular phylogeny. Potential clades with high antimicrobial potential were traced by employing two different methods: organ targeted and biological response based. The latter proved to be more effective. The research presented in this thesis provides new approaches to improve identification, protection against herbivory, and bioprospecting of wild orchids cultivated in botanical gardens and preserved in nature reserves. Show less
Bacterial biocatalysis constitutes a sustainable alternative for high-value chemicals production by enabling the utilization of renewable feedstocks. However, biobased production ofaromatic... Show moreBacterial biocatalysis constitutes a sustainable alternative for high-value chemicals production by enabling the utilization of renewable feedstocks. However, biobased production ofaromatic compounds and biopolymers requires a specialized microbial cell factory. Microbial hosts may experience cell toxicity caused by the solvent-like compounds that emerge as products, substrates or intermediates during the production process. Therefore, solvent tolerance is an essential trait for the microbial hosts used in biobased production of aromatic chemicals and biopolymers. The work described in this thesis focused on identifying and characterizing genes/gene clusters which are involved in conferring solvent tolerance trait in bacteria. Adaptability of P. putida S12 is dependent on the ability to cope with the high energy demand of solvent stress. The inherent metabolic flexibility of P. putida S12 has partly been developed through horizontally transferred traits, such as aromatic degradation pathways and solvent extrusion pumps. Show less
The applications of studying the early development of insects range from agriculture to material science. In agriculture creating new kinds of pesticides and in material science making new... Show moreThe applications of studying the early development of insects range from agriculture to material science. In agriculture creating new kinds of pesticides and in material science making new materials that avoid desiccation. After Drosophila melanogaster, Tribolium castaneum is becoming the most used insect in developmental biology because Tribolium’s development is more representative to the rest of the insects’ development than Drosophila’s. In this thesis the early development of Tribolium is studied, specifically cellularization and serosal window closure. Cellularization is the formation of the cells. We discovered that the mechanical interaction between cells leads to the formation of a Voronoi tilling in the cells’ arrangement. Furthermore, we studied the genetics of cellularization by silencing genes related to junction proteins. We found that Innexin 7 protein is central to finish the process of cellularization. Serosal window closure is the first cell rearrangement to create a cover for the embryo. We looked for proteins involved in serosal window closure. We found that protein Laminin α1,2, β and γ is a key cell component in the process of serosal window closure. In conclusion, during development there are physical and genetics factors acting at the same time. Show less
The soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides... Show moreThe soil-dwelling, filamentous bacteria of the genus Streptomyces are renowned for their production of useful secondary metabolites including antibiotics. The work described in this thesis provides new insights on the role and regulation of antibiotic production and resistance in these bacteria. It shows that antibiotic resistance is already beneficial at sub-inhibitory antibiotic concentrations. Resistance can even readily evolve at such low concentrations, thereby possibly explaining the level of resistance seen in pristine environments. Antibiotic producers can benefit from spatial structure, as present in the soil, through the preferential allocation of resources and this enables invasion from low frequencies. Streptomyces do not produce all antibiotics continuously, but antibiotic production is instead tightly regulated in response to environmental cues, including those produced by competitors. Streptomyces are most likely to induce antibiotic production in response to a competitor that shares similar secondary metabolite clusters, indicating a possible role for shared signalling. Besides changes in antibiotic production, other responses to competition are revealed on a transcriptomic level, including an increased expression of developmental genes, suggesting earlier sporulation. Show less
