Most proteins and their complexes are flexible and dynamic in solution, occupying several conformations over time. Therefore, complex formation can be thought of as following a trajectory along... Show moreMost proteins and their complexes are flexible and dynamic in solution, occupying several conformations over time. Therefore, complex formation can be thought of as following a trajectory along which a loosely associated, weakly interacting encounter complex acts to pre-orient the binding partners before they proceed to the final stereo-specific state. Encounter complexes often play a large role for complexes that must balance a biological requirement for a high turnover rate with the necessity of forming a specific interaction. This is particularly the case for electron transfer complexes, such as the complex between yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). The work described in this thesis focuses on the use of paramagnetic nuclear magnetic resonance (NMR) spectroscopy to study dynamic (transient) protein complexes, using the Cc-CcP complex as a model. Paramagnetic NMR has proven to be an extremely powerful technique for studying lowly populated states such as those of the encounter complex. It relies on the magnetic effects generated by an unpaired electron within a paramagnetic centre that disturb the local magnetic field experienced by nearby nuclei. This results in measureable changes in the NMR signals from which distance and orientation information for protein structure modelling can be extracted. Show less
Current energy-sources in the form of fossil fuels are quickly being depleted, while the demand of energy by society is increasing. In order to sustain this growth in energy demand, alternatives... Show moreCurrent energy-sources in the form of fossil fuels are quickly being depleted, while the demand of energy by society is increasing. In order to sustain this growth in energy demand, alternatives for the production of energy in a usable form are needed. One of such alternatives is to employ photocatalysis in order to use sunlight for the production of chemical fuels such as for example H2 or methanol. For the production of fuels, electrons are required that can be obtained by oxidizing water, as done by nature in a process called photosynthesis. The work in this thesis was inspired by this natural process; photosensitizers and water-oxidation catalysts were bound to lipid bilayers and their ability to photocatalytically oxidize water was studied in different conditions. The anchoring of compounds to a lipid bilayer leads to large differences in reactivity compared to homogeneous systems. In some cases, even the mechanism of the photocatalytic reaction changed upon membrane-anchoring of the constituents. In general, detailed experiments are described that fully characterize photocatalytic systems, because the mechanism of a reaction involving two different catalytic species is not straight-forward, and cannot be described by a single set of turn-over numbers. Show less
The seasonally distinct phenotypic variation in the eyespots of the African Bicyclus anynana is the result of an intriguing system in which ecology, evolution and developmental biology are closely... Show moreThe seasonally distinct phenotypic variation in the eyespots of the African Bicyclus anynana is the result of an intriguing system in which ecology, evolution and developmental biology are closely entangled. This thesis explores the genetic and genomic characteristics of this butterfly by means of cytogenetics, linkage mapping, and QTL analysis to provide a framework that allows a better understanding of the genetic component of eyespot size variation. Cytogenetics uncovered the general chromosome characteristics in this species and also provided intriguing new insights in sex-chromosome evolution. Linkage mapping and QTL analysis located a number of chromosomal regions involved in eyespot size determination, most of which do not coincide with known candidate genes. Therefore, new directions in research on seasonal polyphenism have opened up as a result of these findings. Show less
This research provides a novel, empirically tested, actionable theory of cluster innovativeness. Cluster innovativeness has for long been subject of research and resulting policy efforts. The... Show moreThis research provides a novel, empirically tested, actionable theory of cluster innovativeness. Cluster innovativeness has for long been subject of research and resulting policy efforts. The cluster's endowment with assets, such as specialized labor, firms, research institutes, existing regional networks and a specific culture are, among others, recognized as sources of innovativeness. While the asset structure of clusters as been subject to a variety of research efforts, the evidence on the "soft" factors remains largely anecdotal. This theory building effort aims at providing a comprehensive picture of the contributors to technology cluster innovativeness. In doing so, it applies a dynamic capability framework in combination with a dynamic, network-level research approach in across five European satellite navigation application clusters. It shows that cluster innovation capabilities not only exist, i.e. community building, strategic alignment, reconfiguration, opportunity recognition and networking, but also impact perceived cluster performance. In contrast, the cluster's asset base assumes rather a moderating role. These results and the research approach add to existing theories of regional innovativeness. Furthermore, the research strengthens the dynamic capability view by providing evidence on inter-organizational capabilities. Accordingly, cluster managers and policy makers should focus their activities on their cluster's capabilities in an ongoing optimization process. Show less
In this thesis project, new manganese(III) compounds containing phenol-pyrazole ligands are presented. Small variations on the phenol-pyrazole ligand have been performed to investigate the role of... Show moreIn this thesis project, new manganese(III) compounds containing phenol-pyrazole ligands are presented. Small variations on the phenol-pyrazole ligand have been performed to investigate the role of the ligand in the formation of new complexes. The reaction conditions are also crucial to determine the nuclearity of the obtained compounds, which range from mononuclear to octanuclear compounds. Additionally, the magnetic properties of the synthesized compounds were studied. Magneto-structural correlations are presented to assess the important structural features for tuning the magnetic properties. Show less
Schnitzeler, Dominic Hubertus Franciscus Maria 2008
In this thesis I use the novel technique of Rotation Measure synthesis (RMS) to study the Galactic interstellar medium. With RMS we can study Faraday rotation and synchrotron emission along the... Show moreIn this thesis I use the novel technique of Rotation Measure synthesis (RMS) to study the Galactic interstellar medium. With RMS we can study Faraday rotation and synchrotron emission along the line of sight. I apply RMS to 4 data sets that we obtained with the WSRT. With RMS we can separate the signal of a polarized extragalactic source from the signal from our own Milky Way. Depending on the viewing direction in the Milky Way, the rotation measures of extragalactic sources and diffuse emission (dis)agree. We supplement our observations with MHD simulations of the Galactic ISM, to better understand how we can interpret the observed features as structure in the Galactic ISM and the Galactic magnetic field. Finally, we combined our results with literature values on pulsars, extragalactic sources, and the diffuse emission. We found a way to calculate the electron-density weighted line-of-sight magnetic field strength from the RM and DM that we can either measure or model for these sources. With all this information we determined that the large-scale magnetic field in the second Galactic quadrant shows much more structure than what the currently best available model can predict. Show less
This thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a... Show moreThis thesis describes experiments, in which we used an optical-tweezers setup to study a number of biological systems. We studied the interaction between the E. coli molecular chaperone SecB and a protein that was being unfolded and refolded using our optical tweezers setup. Our measurements clearly showed that in the presence of SecB, an unfolded protein could not refold. Molecular dynamics simulations were used to successfully explain features that were observed in our unfolding experiments. Our approach enables studies on other chaperones, as well. Next, we aimed to study translocation of single proteins through membranes by the E. coli Sec translocase. We modified an often-used model protein for our experiment. Different used experimental strategies are presented. Future experiments should enable measurements on the translocation of a single protein. The last study was on the packaging of double-stranded DNA by a single bacteriophage phi29. We aimed to study the effect of multivalent cations on the negatively-charged, tightly-packed DNA inside the bacteriophage capsid and in that way on the speed of the packaging process. A special DNA molecule was constructed and used in a number of successful packaging experiments. Future experiments should show the effect of cations on the packaging rate. With Summary in Dutch Show less
