This thesis consists of two subjects, that are both a consequence of radiation pressure. In optomechanics, light is used to influence the motion of a trampoline resonator. It is possible to slow... Show moreThis thesis consists of two subjects, that are both a consequence of radiation pressure. In optomechanics, light is used to influence the motion of a trampoline resonator. It is possible to slow down this motion, cooling it from room temperature to an effective temperature of several milllikelvins, The other subject is how superconductivity influences the Casimir force between a niobium-titanium-nitride plate and a gold microsphere. This has been investigated both theoretically and experimentally. Show less
The dissertation describes TEM experiments on heterogeneous catalysts. Starting with characterization of (Ni/Co)MoS2 on Alumina and the effect of oxidation, and sequential resulfidation. After that... Show moreThe dissertation describes TEM experiments on heterogeneous catalysts. Starting with characterization of (Ni/Co)MoS2 on Alumina and the effect of oxidation, and sequential resulfidation. After that, Co-based catalysts are used for high-resolution (S)TEM/EDX caracterization studies, and in situ catalysis experiments. Show less
We investigate how radiation pressure can be used to influence the mechanical motion of a micro-mirror suspended from springs. This trampoline resonator is part of an optical Fabry-Perot cavity. By... Show moreWe investigate how radiation pressure can be used to influence the mechanical motion of a micro-mirror suspended from springs. This trampoline resonator is part of an optical Fabry-Perot cavity. By tuning the laser frequency with respect to the optical resonance, we are able to optically cool the mechanical motion of the resonator. When combining this optical cooling with cryogenic cooling techniques, we are able to bring the mechanical resonator close to the quantum mechanical ground state. This is a requirement for future experiments to investigate the fundamentals of quantum mechanics. Show less
Of all the mass in our Universe, 80% is thought to consist of a hypothetical and invisible substance called dark matter (DM). So far, all observations of DM are based on its gravitational... Show moreOf all the mass in our Universe, 80% is thought to consist of a hypothetical and invisible substance called dark matter (DM). So far, all observations of DM are based on its gravitational interaction, either through the dynamics of normal (baryonic) matter or through the deflection of light. The latter approach, called ‘gravitational lensing’, is a unique way to probe the distribution of DM without making any assumptions on its dynamical state, and on scales larger than the extent of baryons. Using weak gravitational lensing with the Kilo-Degree Survey (KiDS), we first study the relation between galaxies and their dark matter halos on the scale of individual galaxies and galaxy groups. We then attempt to measure the effect of the local and large scale (cosmic web) density distribution on galaxies and halos, and we measure the interplay between galactic and DM structures at the scale of the cosmic web. Finally, we perform the first test of Verlinde’s theory of Emergent Gravity, all with the ultimate goal of gleaning some insight into the possible nature of the elusive ‘missing mass’. Show less
Traditional drug discovery approaches have been hampered by (in vitro) cell-culture models that poorly represent the situation in the human body. Principally, cells grow in the body in a three... Show moreTraditional drug discovery approaches have been hampered by (in vitro) cell-culture models that poorly represent the situation in the human body. Principally, cells grow in the body in a three-dimensional (3D) environment that cannot generally be captured using cell culture methods. For this reason, cell-culture models have been developed where cells grow in a 3D-environment, which allows them to form structures that are more comparable to tissue in the body. However, the full complexity of these advanced cell-culture models can only be fully used for routine drug testing if the cell culture model can be used on a large scale (also termed high-throughput screening or HTS), and if the readout can capture all of the biological complexity reflected by the 3D-cultured cells (high-content screening or HCS). Due to these technological limitations, 3D cellular models are not yet routinely applied in drug and drug-target discovery. This thesis describes the development of fully-scalable 3D cell-culture screening platforms in the context of cancer and polycystic kidney disease. Show less
The main goal of the research described in this thesis was the development of new photoactivated chemotherapy (PACT) ruthenium(II) complexes bearing a non-toxic photolabile ligand. We first... Show moreThe main goal of the research described in this thesis was the development of new photoactivated chemotherapy (PACT) ruthenium(II) complexes bearing a non-toxic photolabile ligand. We first investigated whether non-toxic ligands such as L-proline, 2-(methylthio)methylpyridine (mtmp), or 3-(methylthio)propylamine (mtpa), once coordinated to ruthenium(II) complexes, could be photosubstituted upon visible light irradiation. The lipophilicity, and in some cases the strain of the ruthenium(II) complexes, were systematically varied and the effects of such variations on the cytotoxicity of the complexes in the dark and under light irradiation were studied. In the second part, the best ligand candidates (i.e. mtmp and mtpa) were coordinated to cyclometalated ruthenium complexes of the type [Ru(bpy)(phpy)(S,N)]PF6 (bpy = 2,2’-bipyridine and phpy = 2-phenylpyridine), to shift the absorption of the complex to the red region of the spectrum. The photosubstitution properties of these cyclometallated complexes were investigated in detail. The most promising ruthenium complexes were tested in cancer cell monolayers under hypoxic conditions (1% O2) to investigate their mode of action and distinguish between PACT and PDT. Show less
Drug-target binding kinetics determine the time course of the central event in pharmacotherapy: Drug-target interaction. However, the time course of a drug effect is also influenced by many... Show moreDrug-target binding kinetics determine the time course of the central event in pharmacotherapy: Drug-target interaction. However, the time course of a drug effect is also influenced by many other physiological processes such as the metabolism and excretion of a drug and the transduction of the relevant biological signals. In this study, we investigate when target binding kinetics are determining the time course of drug effect and generate understanding into the relation between the parameter values and the rate-limiting step in the duration of a drug effect. Show less
Cardiovascular diseases are among the most frequent causes of death in the world. The main underlying pathology of cardiovascular diseases is the development of atherosclerosis in the medium and... Show moreCardiovascular diseases are among the most frequent causes of death in the world. The main underlying pathology of cardiovascular diseases is the development of atherosclerosis in the medium and large-sized arteries. The role of several immune cell subsets has been identified in atherosclerosis and it has been established that the immune system contributes to initiation and progression of cardiovascular diseases. Atherosclerosis is thus currently described as a chronic inflammatory disease and both the innate and adaptive immune cells contribute to disease initiation and progression. This suggests that targeting the ongoing inflammatory response may limit atherogenesis. This thesis discusses several therapeutic immune targets to limit atherosclerotic lesion development. The results described show the interplay between lipids and the immune system and a number of anti-inflammatory strategies to reduce atherosclerotic lesion development. The studies show a clear advantage of reducing inflammation in atherosclerotic lesion development. Future (clinical) studies identifying new targets will lead to a better-personalized therapy reducing atherosclerosis. Show less
Planets are formed in disks of gas and dust around young stars. These planet-forming disks undergo several physical and chemical processes that can lead to planetary systems like our own. This... Show morePlanets are formed in disks of gas and dust around young stars. These planet-forming disks undergo several physical and chemical processes that can lead to planetary systems like our own. This thesis uses data of two well known planet-forming disks around TW Hya and HD 163296 taken with the Atacama Large (sub)Milimeter Array (ALMA) and the Herschel Space Telescope to study the spatial distribution of their dust and gas content. In particular, we aim to constrain the spatial distribution of the main oxygen- and nitrogen-bearing species in planet-forming disks and to explore the relationship between their physical features and the formation and chemistry of common molecular species. By analysing water and ammonia emission form the disk around TW Hya, we conclude that the location of oxygen- and nitrogen-bearing volatiles in planet-forming disks are set by grain evolution, in particular radial drift. In addition, we conclude that the spatial location of temperature-sensitive species trace substructures in the temperature profile of protoplanetary disks and therefore (indirectly) the impact of dust evolution process on its morphology. Show less
There is an urgent need for more physiologically relevant cell culture methods to guide compound selection in pre-clinical stages of the drug development pipeline. This thesis describes the... Show moreThere is an urgent need for more physiologically relevant cell culture methods to guide compound selection in pre-clinical stages of the drug development pipeline. This thesis describes the development of the OrganoPlate, a microfluidic platform that enables enhanced physiology in cell culture models by combining 3D cell culture, co-culture and perfusion flow, whilst maintaining ease of use, compatibility and throughput. Phaseguides are capillary pressure barriers that enable microfluidic liquid routing and patterning without the use of membrane or other physical barriers. This technology was further developed to enable complex liquid routing using only a standard pipette Phaseguide technology was implemented for gel patterning in a dedicated 3D cell culture device embedded in a standard 384 wells plate. Each plate contains up to 96 microfluidic networks that enable perfusion culture of extracellular matrix embedded tissues and perfused epithelial or endothelial tubules. The standard dimensions and high quality optical readout allows interrogation of these tissues using high content readers as well as other standard readout equipment. The platform has been used for the culture of a variety of tissue types and disease models by the authors, but has also been adopted by expert and non-expert users across the field. Show less
In this thesis chemical and physical processes in the ice mantles on interstellar dust grains are studied. With the Atacama Large Millimetre/submillimetre Array molecules of interest to the... Show moreIn this thesis chemical and physical processes in the ice mantles on interstellar dust grains are studied. With the Atacama Large Millimetre/submillimetre Array molecules of interest to the formation of bigger, life-bearing molecules are detected for the first time around the sun-like low-mass protostar IRAS 16293-2422. These detections give clues about the earliest conditions our solar system formed under and potentially how life on earth emerged. Laboratory studies investigate the formation of these complex species in a laboratory set-up mimicking the conditions on interstellar icy dust grains. In this ways formation routes for molecules with a so-called amide functional group are mapped. Show less
Plants and their pollinators form complex interaction networks. Within these networks, species differ widely in the number of species they interact with. These interaction patterns are important... Show morePlants and their pollinators form complex interaction networks. Within these networks, species differ widely in the number of species they interact with. These interaction patterns are important aspects in pollination ecology, since it influences species coexistence and community stability. An in-depth understanding of the mechanisms behind plant-pollinator interactions is thus important to predict the dependency of species on each other and responses of plant-pollinator communities to (global) changes, such as the introduction of invasive species and climate change. In this study, I investigated whether flower abundance, flower morphology (nectar tube depth and flower display area), nectar production and pollinator foraging efficiency can predict plant-pollinator interaction patterns and the stability of these interactions. This study shows that flower density might be less important for structuring plant-pollinator interactions. Pollinators do not forage randomly. Rather flower morphology, nectar production and pollinator foraging efficiency are important aspects that determine interaction patterns, including species generalization degree and matching between flower nectar tube depth and pollinator proboscis length (size-matching). Although plant species with deeper flowers are more specialized, they are visited by pollinator species which, locally, fluctuate less across years. Thus, specialized plants might be less vulnerable to yearly fluctuations in plant-pollinator communities than often assumed. Show less
In recent decades, the use of a systems-based view of life has provided key insight into fundamental processes with respect to biology. In life sciences, important paradigm shifts are the way in... Show moreIn recent decades, the use of a systems-based view of life has provided key insight into fundamental processes with respect to biology. In life sciences, important paradigm shifts are the way in which we approach health and disease. Although modern medicine has traditionally emphasized pathology and acute conditions, our current understanding is that different interventions are needed for treating and preventing chronic disease. To design better interventions, new diagnostic tools are urgently needed in order to create new opportunities for achieving personalized health and medicine. The focus in diagnosis is, therefore, shifting from measuring single biomarkers such as glucose and cholesterol to creating complex maps of the dynamic patterns underlying regulatory processes. Moreover, the notion of "health" is viewed in a holistic context using biochemistry as a basis and then expanding this basis to include the psycho-social environment, including the individual's worldview. In the field of diagnostics, a highly promising new tool has recently emerged based on ultra-weak photon emission from biological systems, including all living cells. The aim of this thesis was to explore the applications of UPE and correlate it with biochemistry in order to obtain a deeper understanding of the processes that occur in living systems. Show less
Conventional chemotherapy often suffers from a lack of specificity, affecting both normal and cancer cells. Light-activated drugs provide spatial and temporal control over their activity, providing... Show moreConventional chemotherapy often suffers from a lack of specificity, affecting both normal and cancer cells. Light-activated drugs provide spatial and temporal control over their activity, providing a possible solution for this problem. This dissertation describes the synthesis and biological applications of (blue/green/red) light-activated ruthenium polypyridyl drugs as potential prodrugs against cancer. Show less
Cardiovascular disease (CVD) due to atherosclerosis is a major cause of death. In atherosclerotic lesions, two major types of macrophages can be distinguished: 1) pro-inflammatory M1-macrophages... Show moreCardiovascular disease (CVD) due to atherosclerosis is a major cause of death. In atherosclerotic lesions, two major types of macrophages can be distinguished: 1) pro-inflammatory M1-macrophages, which promote atherosclerosis and 2) anti-inflammatory M2-macrophages, which are regarded athero-protective. Hence, skewing of macrophages from an M1 to an M2-phenotype might be a promising alternative therapeutic strategy against CVD. In this PhD dissertation, using the bone marrow transplantation (BMT) technique, we examined several genes that were hypothesized to be promising drug targets to favorably modulate macrophage phenotype and function, including the classic M2 marker gene Arginase 1 (Arg1), the key regulators of M2-macrophage activation Akt2 (AKT Serine/Threonine Kinase 2) and MKP2 (MAP Kinase Phosphatase 2), and Usf1 (upstream stimulatory factor 1). Although we were successful in skewing macrophages into an M2-phenotype, this also led to accelerated foam cell formation, which counteracted the anti-inflammatory athero-protective effects of the M2-macrophage thereby limiting its therapeutic value. Overall this work underlines that modulation of macrophage polarization in atherosclerosis is feasible. However, more research is required to identify the key beneficial regulators and their overall effects in the complex microenvironment of atherosclerotic plaque before macrophage polarization can be exploited as an alternative therapeutic strategy against CVD. Show less
This Thesis describes the design, synthesis and evaluation as glycoprocessing enzyme inhibitors of focused libraries of iminosugars. In the studies described, 1-deoxynojirimycin (DNJ), and its... Show moreThis Thesis describes the design, synthesis and evaluation as glycoprocessing enzyme inhibitors of focused libraries of iminosugars. In the studies described, 1-deoxynojirimycin (DNJ), and its known N-alkylated derivatives, served as starting points. DNJ modifications presented here include alteration of the substitution pattern of the piperidine core structure; variation in the N substituent, or a combination of the two. Biological evaluation of the synthesized compounds focused on the glycoprocessing enzymes involved in glucosylceramide metabolism: glucosylceramide synthase (GCS), lysosomal glucosylceramidase (GBA1) and neutral glucosylceramidase (GBA2), and in all examples presented the inhibitory potency of newly synthesized compounds are compared with that of literature compounds. Show less
In this thesis we will explore the use of fuzzy systems theory for applications in bioinformatics. The theory of fuzzy systems is concerned with formulating decision problems in data sets that... Show moreIn this thesis we will explore the use of fuzzy systems theory for applications in bioinformatics. The theory of fuzzy systems is concerned with formulating decision problems in data sets that are ill-defined. It supports the transfer from a subjective human classification to a numerical scale. In this manner it affords the testing of hypothesis and separation of the classes in the data. We first formulate problems in terms of a fuzzy system and then develop and test algorithms in terms of their performance with data from the domain of the life-sciences. From the results and the performance, we will learn about the usefulness of fuzzy systems for the field, as well as the applicability to the kind of problems and practicality for the computation itself. Show less
Cardiovascular syndromes are the major cause of death in Western societies. The main underlying pathology is atherosclerosis, a chronic disease affecting the arteries. During atherosclerosis... Show moreCardiovascular syndromes are the major cause of death in Western societies. The main underlying pathology is atherosclerosis, a chronic disease affecting the arteries. During atherosclerosis progression, LDL, or “bad” cholesterol, accumulates in the arterial wall, resulting in the formation of a lipid-rich atherosclerotic plaque. This event activates the immune system, which increases plaque inflammation. Mast cells are components of the immune system known for their role in allergy. However, it has been established that mast cells are also important in atherosclerosis. In this PhD dissertation, we explored the interaction of mast cells with other immune cells. We examined the interrelation between mast cells and T-lymphocytes and discovered that mast cells can function as antigen presenting cells in atherosclerosis and, enhance the development of an atherosclerotic plaque via a direct interaction. Nonetheless, mast cells can also act on the Natural Killer T-cells, resulting in a protective function against atherosclerosis. Importantly, we used a relatively novel technical approach to explore the characteristics of mast cells inside human atherosclerotic plaques. We found that mast cells are highly activated and thus possibly promote disease progression. In conclusion, mast cells possess both protective and harmful effects, acting as regulators of the immune response in atherosclerosis. Show less
Microbial rhodopsins are photosensitive pigments implemented in the growth and adaptation of a large population of microorganisms. These relatively simple, tunable photosystems use a molecule... Show moreMicrobial rhodopsins are photosensitive pigments implemented in the growth and adaptation of a large population of microorganisms. These relatively simple, tunable photosystems use a molecule of retinal as a chromophore to facilitate the conversion of sunlight to chemical energy. Retinal-based phototrophy is believed to sustain the phototrophic balance of various biospheres and has several important biotechnological applications. In this thesis, we propose the use of microbial rhodopsins as an alternative photosystem in a complementary approach towards more efficient use of photons in the solar spectrum. Towards this end, we describe the adaptation of two rhodopsin proton-pumps, namely proteorhodopsin and Gloeobacter rhodopsin, to shift their action spectrum into the near-infrared region. Several red-shifted variants of were generated by utilizing a combination of retinal analogs with specific opsin mutations. We also constructed a novel directed-evolution set-up, which allows us to generate a library of red-shifted mutants with simultaneous screening for spectral shifts and proton-pumping ability. Finally, the impact of a detergent or lipid microenvironment was tested on the various pigments generated in this study. Our results have important prospects in a number of biotechnological fields such as optogenetics, membrane-sensor technology and as a complementary photosystem for oxygenic photosynthesis. Show less
Self-assembly is an abundant process in nature and is vital to many processes in living organisms. During the last decade the fields of supramolecular chemistry and polymer science have made... Show moreSelf-assembly is an abundant process in nature and is vital to many processes in living organisms. During the last decade the fields of supramolecular chemistry and polymer science have made an integrated effort in the design, synthesis and application of supramolecular polymers. Supramolecular polymers rely on relatively weak non-covalent interactions such as hydrogen bonding, solvophobicity and π-stacking to self-assemble using a wide array of natural and artificially designed interaction motifs. Using these principles, both end-functionalized polymers interacting via molecular recognition and stacked monomers self-assembling into one-dimensional structures have been demonstrated. A uniquely naturally-occurring supramolecular polymer is DNA which, apart from its role in genetics, can be used as a building block for both structural and dynamic applications such as making well-organized three-dimensional lattices or reconfigurable and autonomously operating DNA-based devices. As every class of materials has their own advantages, designing multicomponent materials from multiple types of building blocks such as DNA, and supramolecular and covalent polymers, has the potential to create highly advanced, organized and responsive materials both from structural and functional points of view. This dissertation has focused on designing such multicomponent functional supramolecular materials for biomedical applications and diagnostics. Show less
