The sequence-dependence of biomolecular interactions involving nucleic acids and proteins is essential for numerous processes inside the cell. Insights into the underlying molecular mechanisms have... Show moreThe sequence-dependence of biomolecular interactions involving nucleic acids and proteins is essential for numerous processes inside the cell. Insights into the underlying molecular mechanisms have been obtained using various biochemical and biophysical methods on two different levels — bulk and single-molecule. These have complemented each other as single-molecule studies excel in observing multi-state dynamic interactions, but perform only at low throughput; while bulk studies can probe many different sequences simultaneously, but providing limited kinetic information. To unite the strengths of both levels, we developed high-throughput Single-molecule Parallel Analysis for Rapid eXploration of Sequence space (SPARXS), that allows the study of molecular structure, kinetics and interactions for thousands of different sequences simultaneously at the single-molecule level. We, for the first time, combine single-molecule fluorescence with next-generation Illumina sequencing. As a proof of principle we apply SPARXS to study the sequence-dependent kinetics of the four-way DNA Holliday junction, occurring among others during homologous recombination. Using SPARXS we observe the dynamic behavior of 120,000 Holliday junction molecules covering 3750 distinct core sequences, a result unattainable with previous techniques. Overall, the mechanistic insights obtained using SPARXS will give an entirely new view on the relationship between sequence, structure and function. Show less
Tin electrodeposition applications have rapidly evolved in the past 25 years. Usage of tin coatings has advanced from being mainly used for corrosion protection and decorative purposes, to being... Show moreTin electrodeposition applications have rapidly evolved in the past 25 years. Usage of tin coatings has advanced from being mainly used for corrosion protection and decorative purposes, to being used in modern technology such in electronic devices, photovoltaic cells and Li-ion batteries. The new tin coating applications have also come with challenges that require the production of nanostructured deposits, multilayers coatings and composites. Furthermore, the need to reduce energy and source consumptions, and the implementation of more environment-friendly processes, require detailed and fundamental knowledge of the electrodeposition process.The emphasis throughout this thesis is therefore to obtain detailed mechanistic information of tin electrodeposition process.The experimental and theoretical work presented in this thesis attempts to understand the mechanism of tin electrodeposition, and the effect of electrolyte anions and naphthalene-based additives, during the early and subsequent stages of the process. Show less
During the course of drug discovery translational steps are made. The translation from in vitro to in vivo experiments is not as predictive as one would desire, resulting in selection of... Show moreDuring the course of drug discovery translational steps are made. The translation from in vitro to in vivo experiments is not as predictive as one would desire, resulting in selection of inefficacious compounds but also in overlooking of promising drug candidates. This is not different for the mGlu2 receptor for which no drugs are available on the market so far despite enormous drug discovery efforts. Therefore, there is a need to improve the molecular understanding of key in vitro parameters that drive in vivo efficacy. Hence, this thesis focuses on the concepts of target binding kinetics and functional efficacy of both allosteric and orthosteric ligands of the mGlu2 receptor. Show less
Prion diseases are fatal neurodegenerative disorders associated with the polymerization of the cellular form of prion protein (PrP(C)) into an amyloidogenic β-sheet infectious form (PrP(Sc)). The... Show morePrion diseases are fatal neurodegenerative disorders associated with the polymerization of the cellular form of prion protein (PrP(C)) into an amyloidogenic β-sheet infectious form (PrP(Sc)). The sequence of host PrP is the major determinant of host prion disease susceptibility. In mice, the presence of allele a (Prnp(a), encoding the polymorphism Leu-108/Thr-189) or b (Prnp(b), Phe-108/Val-189) is associated with short or long incubation times, respectively, following infection with PrP(Sc). The molecular bases linking PrP sequence, infection susceptibility, and convertibility of PrP(C) into PrP(Sc) remain unclear. Here we show that recombinant PrP(a) and PrP(b) aggregate and respond to seeding differently in vitro. Our kinetic studies reveal differences during the nucleation phase of the aggregation process, where PrP(b) exhibits a longer lag phase that cannot be completely eliminated by seeding the reaction with preformed fibrils. Additionally, PrP(b) is more prone to propagate features of the seeds, as demonstrated by conformational stability and electron microscopy studies of the formed fibrils. We propose a model of polymerization to explain how the polymorphisms at positions 108 and 189 produce the phenotypes seen in vivo. This model also provides insight into phenomena such as species barrier and prion strain generation, two phenomena also influenced by the primary structure of PrP. Show less
Huidig beleid schrijft voor dat voor de bloedtransfusie plaatsvindt, het serum van de patient getest wordt op irreguliere anti-stoffen van rode bloedcellen. In dit boek onderzoekt Henk Schonewille... Show moreHuidig beleid schrijft voor dat voor de bloedtransfusie plaatsvindt, het serum van de patient getest wordt op irreguliere anti-stoffen van rode bloedcellen. In dit boek onderzoekt Henk Schonewille of dit beleid moet veranderen om bloedtransfusie veiliger te maken. Current pre-transfusion policy requires the patient's serum to be tested for the presence of irregular red blood cell antibodies. In case of an alloantibody, red blood cells lacking the corresponding antigen are transfused after an antoglobulin crossmatch. The aim of the study in this thesis is primarily to investigate whether this policy should change to improve transfusion safety Show less
