Photosynthesis is the physico-chemical process by which plants, algae and photosynthetic bacteria use light energy to drive the synthesis of organic compounds. Light-induced electron transfer in... Show morePhotosynthesis is the physico-chemical process by which plants, algae and photosynthetic bacteria use light energy to drive the synthesis of organic compounds. Light-induced electron transfer in photosynthetic reaction centers (RCs) is highly efficient, having a quantum yield close to unity. In RCs of Rhodobacter (R.) sphaeroides wild type (WT), the primary electron donor is a bacteriochlorophyll a (BChl) dimer, called the Special Pair P, comprising two dimer halves PL and PM. Two additional BChl cofactors called accessory BChls (BA and BB), two bacteriopheophytins (_A and _B), two quinones and a non-heme iron are organized into two pseudo-symmetric branches named A and B. After the photo excitation the electron is transferred only via the active __A__ branch. On the other hand, in structurally similar RCs, as that of photosystem I, the electron transfer occurs equally over both branches. Neither the reason for the high efficiency nor that of the directionality of the electron transfer has been elucidated so far. To solve these questions, the solid-state photo-chemically induced nuclear polarization (photo-CIDNP) effect with its dramatic enhancement of local NMR signals provides an analytical tool especially suited for studying electron transfer in photosynthetic RCs. In fact, photo-CIDNP MAS NMR has been applied to explore electronic structures of the electron donors and acceptors in RCs Show less
Programmed ribosomal frameshifting (PRF) is one kind of recoding events that is mostly utilized by RNA viruses to synthesize more proteins with defined ratio from their compact genome and it is... Show moreProgrammed ribosomal frameshifting (PRF) is one kind of recoding events that is mostly utilized by RNA viruses to synthesize more proteins with defined ratio from their compact genome and it is known that the stoichiometric is critical to virus infection and propagation. Two cis-acting RNA elements are critical to induce PRF: one is slippery sequence where the frameshifting occurs and the other is RNA secondary structure, either a stem-loop or pseudoknot, to stall ribosomes on the slip site. In this thesis, we first demonstrate that a stem-loop structure can efficient replace pseudoknot in inducing frameshifting, arguing previous assumption hairpins are efficient frameshiftors. Furthermore, we show antisense oligonucleotides (AON) that mimic hairpin or pseudoknot can promote efficient frameshifting suggesting the downstream secondary structures act as physical barriers in frameshifting. Finally, we report a novel ligand responsive frameshifting signal derived from non-frameshifting preQ1 riboswitch aptamer. This interesting finding may have potential to select compounds with anti-bacteria ability. In sum, we successfully use in trans AONs or metabolites to induce PRF. These findings not only address fundamental mechanism of PRF but have potential to develop drugs against frameshifting diseases or bacteria. Show less
This Thesis aims at the development of novel subunit selective inhibitors of the proteasome. -Three vinyl sulfone analogues of three epoxyketone containing inhibitors described in literature are... Show moreThis Thesis aims at the development of novel subunit selective inhibitors of the proteasome. -Three vinyl sulfone analogues of three epoxyketone containing inhibitors described in literature are synthesised and characterised. The nature of the electrophile determines subunit selectivity of the inhibitor. -Ten Michael acceptors are coupled to three peptoid tails yielding thirty peptide-like compounds. None of the peptoid Michael acceptors are efficient proteasome inhibitors. Using the Staudinger-Bertozzi ligation followed by affinity purification, tryptic digestion of the isolated proteins and LC/MS/MS identification, the targets of two compounds in HEK293T and RAW264.7 cells are determined. -Syringolins are potent proteasome inhibitors found in nature. A syringolin structural motif was built in peptoid epoxyketones and vinyl sulfones yielding a 16-membered library of proteasome inhibitors. The distance between the urea and electrophile dictates subunit selectivity. -Three cyclooctynes are compared to the Staudinger-Bertozzi two-step labelling strategy. Cyclooctynes quantitatively convert azide labelled proteasomes at a lower concentration than the Staudinger-Bertozzi phosphane but cyclooctyne two-step labelling is associated with tremendous background labelling. -A library of peptoid vinyl sulfones with basic amino acid side chains is synthesised. A compound with two benzylamine residues is a potent and _2 selective proteasome inhibitor. Attachment of a BODIPY fluorophore yielded a _2 selective probe. Show less
Aromatic isocyanates are annually produced on the megaton scale from nitro arenes. A major problem with current synthetic strategies is that they utilize the extremely toxic phosgene to carbonylate... Show moreAromatic isocyanates are annually produced on the megaton scale from nitro arenes. A major problem with current synthetic strategies is that they utilize the extremely toxic phosgene to carbonylate a reduced nitroaromatic. More sustainable strategies have been known for decades, in particular the palladium catalyzed reductive carbonylation of nitro arenes with CO in methanol. The lack of a clear mechanistic understanding of this reaction, however, has thus far hampered the development of sufficiently active and selective catalysts; the generation of such understanding is therefore the prime aim of this thesis. Thus, the palladium catalyzed reductive carbonylation of nitrobenzene with CO in methanol was studied in detail, wherein palladium was supported by a variety of diphosphane ligands of different steric and electronic nature. The general mechanistic pictured that emerged form these studies, is that nitrobenzene reduction chemistry is catalytically coupled with methanol oxidation chemistry by a complex network of catalytic reactions that are centred around a palladium-imido complex (__P2Pd2+=NPh__). This catalytic coupling provided a unique opportunity to gather mechanistic insights for both reactions, but also makes the system needlessly complicated when only nitrobenzene carbonylation products are desired. Several other nucleophiles were considered and 2,2,2-trifluoroethanol was identified as promising alternative to methanol. Show less
In this dissertation, I investigate new approaches relevant to content-based image retrieval techniques. First, the MOD paradigm is proposed, a method for detecting salient points in images. These... Show moreIn this dissertation, I investigate new approaches relevant to content-based image retrieval techniques. First, the MOD paradigm is proposed, a method for detecting salient points in images. These salient points are specifically designed to enhance image retrieval accuracy by maximizing distinctiveness. Second, the multi-dimensional maximum likelihood similarity measure is presented, which removes a critical limitation in prior research in this area and provides an improved method of comparing image features. Third, a texture classification method based on low dimensional constructed texture features is introduced which have very low computational complexity and would be suitable for real time video understanding or interactive search of very large image databases. The new approaches are tested on well respected international test sets containing representative imagery. Show less
The main goal of this thesis is to investigate the possible factors playing a role in dilatation of the neo-aortic root in patients after ASO for TGA. Basic histological research as well as... Show moreThe main goal of this thesis is to investigate the possible factors playing a role in dilatation of the neo-aortic root in patients after ASO for TGA. Basic histological research as well as histological 3D reconstruction of the arterial roots has been combined with clinical investigation. The studies that resulted from this research form the basis of this thesis. We went __back to the roots__. Show less
Cancer is one of the leading causes of death worldwide. Treatment is hampered by an incomplete understanding of the mechanisms underlying carcinogenesis and, consequently, by the absence of... Show moreCancer is one of the leading causes of death worldwide. Treatment is hampered by an incomplete understanding of the mechanisms underlying carcinogenesis and, consequently, by the absence of therapies to specifically eradicate cancer cells without harming normal, healthy cells. Intriguingly, the avian-virus derived protein apoptin was found to selectively induce apoptosis in transformed and tumor cells, heralding the advent of a new era in cancer treatment. The aim of this thesis was to discover the path followed by apoptin to distinguish between normal and cancer cells, and selectively kill the latter, in order to a) get to the root of the problem that is cancer, and b) provide the knowledge which is necessary to design novel, more selective, more effective, safe anti-tumor therapies. To this end, we identified a number of apoptin-interacting proteins, and studied their roles in tumor-selective apoptin-induced apoptosis. Show less
In many patients drugs do not show the expected efficacy, whereas in other patients they cause toxic effects, sometimes even at low dose. Response rates to major classes of drugs range from 25 to... Show moreIn many patients drugs do not show the expected efficacy, whereas in other patients they cause toxic effects, sometimes even at low dose. Response rates to major classes of drugs range from 25 to 60 percent. For some patients, the reason for this variability may be explained by genetic variation. Pharmacogenetics is the study of variations in DNA sequence as related to drug response. The ultimate goal of pharmacogenetics is to predict and thereby improve drug response in the individual patient. The concept of interindividual differences in drug response was proposed as early as 1909. With the completion of the Human Genome Project in 2003 hope was raised that pharmacogenetics could be implemented in clinical practice in the near future. However, the clinical use of pharmacogenetic testing remained limited. Yet, the body of evidence supporting its usefulness is growing continuously. The research presented in this thesis aims to identify the reasons for the slow clinical translation of pharmacogenetics and to explore and expand possible solutions to address these obstacles. The thesis is divided into four parts. First, obstacles and possible solutions for the clinical implementation of pharmacogenetics are identified. In the second part, issues related to the quality control of pharmacogenetic testing are discussed. In the third part, the influence of genetic variation on the response to sulfonylureas is used as a case model to investigate the possibilities for pharmacogenetics in primary care. The fourth part contains the general discussion and a future outlook. Show less
In this thesis the role and regulation of the negative p53 regulator Hdmx (Mdmx/Mdm4) are the main topics. Whereas the role of its close homolog Hdm2 is elaborately studied, the function of Hdmx in... Show moreIn this thesis the role and regulation of the negative p53 regulator Hdmx (Mdmx/Mdm4) are the main topics. Whereas the role of its close homolog Hdm2 is elaborately studied, the function of Hdmx in tumourigenesis less understood. Post-translational modification of Hdmx is abundant and may play an important role in the regulation of it function. However, relatively little is known about the nature of these modifications. The aim of this thesis was to provide more insight in the putative oncogenic role of Hdmx and to elucidate some of the mechanisms by which Hdmx function is regulated. Chapter 1 introduces the p53 pathway and it describes the main aspects of the regulation of p53 by Hdm2 and Hdmx. In Chapter 2 the present knowledge about the regulation of Hdmx in relation to the p53 response is presented. Chapter 3 describes the effects of c-Abl mediated phosphorylation on tyrosine residues 55 and 99 of Hdmx, which both modulate the interaction with p53. In chapter 4 the oncogenic functions of Hdmx have been investigated, using an in vitro transformation model of human primary fibroblasts and embryonic retinoblasts. The function of Hdmx overexpression and alternative splicing in osteosarcoma is described in Chapter 5. A model for a role of Hdmx in early tumours and loss of Hdmx in later stage tumours is proposed, with a key role for the change in ratio between the expression of the alternative Hdmx splice variant, Hdmx-S and full length Hdmx. Chapter 6 shows that p53 and its regulators Hdm2 and Hdmx are SUMOylated and ubiquitinated and how the SUMO-specific ubiquitin E3 ligase RNF4 might be involved in these processes. In chapter 7 the function of the FAU gene, encoding the ubiquitin-like protein FUBI and the ribosomal S30 protein, has been studied in osteosarcoma cells. Chapter 8 is a general discussion and provides a summary of the thesis. Show less
The aim of this dissertation is to construct and explore artificial oxygen evolving complexes that are synthetically accessible, stable, functionally robust and efficient. To achieve this, a class... Show moreThe aim of this dissertation is to construct and explore artificial oxygen evolving complexes that are synthetically accessible, stable, functionally robust and efficient. To achieve this, a class of mono metal water splitting catalysts is introduced in this manuscript and exploitation of these complexes in homogeneous catalysis and in electrochemical studies with surface immobilized catalyst assemblies has been discussed. The catalysts are comprised of a single centre ruthenium or iridium metal core coordinated to a dinitrogen ligand and stabilized by a cyclic conjugated hydrocarbon. Homogeneous catalytic water oxidation is performed with a chemical oxidant as catalyst activator. For electro-assisted experiments, the catalyst complexes are functionalized with carboxylic or phosphonic acid linker units on the dinitrogen ligand that serve as anchoring sites for deposition on conducting oxide electrodes. The electrochemical water splitting systems with molecular catalysts have potential application in e.g. rooftop devices to make personalized energy carriers. The proposed __Artificial Leaf__ will soon be the future outcome of the present day technology and efforts in this field. Cheap and easy accessible hydrogen will not only serve as fuel for transportation but also as driving force for green power generation. Show less
In this thesis an interferometric study of diffuse radio sources, so-called halos and relics, in and around galaxy clusters is performed. These sources are thought to trace shocks and turbulence... Show moreIn this thesis an interferometric study of diffuse radio sources, so-called halos and relics, in and around galaxy clusters is performed. These sources are thought to trace shocks and turbulence generated by galaxy cluster merger events. GMRT, WSRT and VLA observations are analyzed to measure the spectral and polarimetric properties of the diffuse cluster emission. In addition, a search for new relics and halos is carried out based on existing radio surveys. Numerical simulations of cluster mergers are described, which have the aim of constraining the cluster mergers parameters from observations of double radio relics. The first LOFAR observation of cluster-scale diffuse radio emission is presented. LOFAR is a new pan-European radio telescope that operates at the lowest radio frequencies accessible from the surface of the Earth. Show less
Spiking neural P systems are a class of distributed and parallel computing models inspired by the neurophysiological behavior of neurons sending electrical impulses (spikes) along axons to other... Show moreSpiking neural P systems are a class of distributed and parallel computing models inspired by the neurophysiological behavior of neurons sending electrical impulses (spikes) along axons to other neurons. In this thesis, we consider that the spiking neural P systems are universal even if the systems work in limited asynchronous mode. And we also investigated different variants of spiking neural P systems with other additional features, such as the axon functioning, the growth of dendritic trees in neurons, the positive or negative weights on synapses, and the astrocytes having excitatory and inhibitory influence on synapses. Show less
Michel Foucault’s work concerned ‘subjectivation’. Contemporary critics argue that his work on ‘surveillance societies’ is based on the industrial organisation paradigm. In the information era, his... Show moreMichel Foucault’s work concerned ‘subjectivation’. Contemporary critics argue that his work on ‘surveillance societies’ is based on the industrial organisation paradigm. In the information era, his surveillance model is said to be defunct. One way of assessing the value of Foucault’s work for present-day concerns is to examine how ‘subjectivation’ relates to technology. His own research on neoliberalism provides a starting-point. We do need to look further though, for example at Bruno Latour’s work, which claims that technologies are to people what ‘plug-ins’ are to the internet. The question is how technology-mediated subjectivation turns out in practice. This study examines the case of healthcare innovation from the point of view of ‘shaping’ the patient. The Dutch Electronic Health Record and the Personal Healthcare Budget are political designs to foster innovation. Both designs were introduced in the mid-1990s and were nearly abolished in 2011. What happened over the course of one and a half decades? The study concludes by examining the democratisation of healthcare innovation in ‘Living Labs’: local or regional platforms in which people are in some way involved in innovation processes. Again, the crucial question is: what roles are attributed to the patient? Show less
We develop the theory of layered Euclidean spaces and layered lattices. We present algorithms to compute both Gram-Schmidt and reduced bases in this generalized setting. A layered lattice can be... Show moreWe develop the theory of layered Euclidean spaces and layered lattices. We present algorithms to compute both Gram-Schmidt and reduced bases in this generalized setting. A layered lattice can be seen as lattices where certain directions have infinite weight. It can also be interpreted as the natural objects to be identified with the cusps of de moduli spaces of lattices. In this thesis the theory of layered lattices is put forward together with algorithm to compute with them and applications. Show less
Quality of the rice grain is determined mainly by starch and protein contents of the endosperm. In this thesis, the analyses of four genes involved in the regulation of development of rice grain... Show moreQuality of the rice grain is determined mainly by starch and protein contents of the endosperm. In this thesis, the analyses of four genes involved in the regulation of development of rice grain and floret are presented. Two CCCH type zinc finger proteins, OsGZF1 and OsGZF2, were identified as novel transcription factors for GluB-1, one of the major seed-storage protein genes. Both of them exhibited negative effects on the GluB-1 promoter in transient expression assays. In a collection of rice mutants, two Tos17 transposon lines were identified showing open-staying florets and abnormal seed development. The mutant gene was identified as OsJAR1 and was shown to encode a jasmonic acid-amino acid synthetase. Next, we identified the potassium antiporter OsCHX14 as one of the downstream genes of OsJAR1. Yeast complementation assays confirmed that OsCHX14 is capable of effluxing K+ outside of cells. Its potential role in regulating of floret closure in rice was discussed. Show less
Present-day embedded software systems need to support an increasing number of features and formalisms; the two most important ones being handling of real-time, and the possibility to develop the... Show morePresent-day embedded software systems need to support an increasing number of features and formalisms; the two most important ones being handling of real-time, and the possibility to develop the system in a modular, component-based way. To ensure that the behaviour of the final system is correct and safe, it needs to be verified before it is being put into operation. This requires formal models to model the system, and formal methods to analyse the formal model and verify certain properties of it. In this thesis, we propose both formal models and formal methods for component-based real-time systems and their coordination patterns. We present a translation from a number of formal models into a representation in propositional logic with linear arithmetic, which allows to use well-established SAT and SMT solver tools to analyse the underlying system. We present an abstraction technique on the representation, that increases the manageable system size by removing parts that are considered irrelevant to the verification of a particular property. We prove the applicability and usability of our framework with a tool implementation, that supports the design and analysis process of component-based real-time systems. Show less
The ongoing research in the field of lysosomal storage diseases (LSD), and more specific Gaucher disease is the basis for the research described in this thesis. The progress of Gaucher disease and... Show moreThe ongoing research in the field of lysosomal storage diseases (LSD), and more specific Gaucher disease is the basis for the research described in this thesis. The progress of Gaucher disease and the effect of therapeutic intervention is correlated to the level of chitotriosidase (CHIT1), the first identified human chitinase. Mea- surement of plasma CHIT1 activity in man is done by an assays using a fluorogenic substrate. The ability of CHIT1 to transglycosylate can complicate the enzyme assay, however umbelliferone 4__-deoxychitobioside is not prone to be transglycosylated. And gives a proportional fluorophore to active enzyme ratio read-out. Because of this umbelliferone 4__-deoxychitobioside has become a popular fluorogenic substrate for the measurement of human chitinases, an improved scalable route towards this compound is described in Chapter 2. Chapter 3 describes the synthesis and biological evaluation of three novel fluorogenic substrates, containing substituents of different sizes on the 4__-OH of the non-reducing sugar. The locally elevated activity of CHIT1 allows sitespecific drug delivery via the prodrug approach. Chapter 4 describes the design and synthesis of novel prodrugs in which a chitobiose core, the substrate for CHIT1, is coupled to known inhibitors of GCS which are able to restore the influx/efflux balance of GC in Gaucher cells. It is known that some iminosugars and N-alkylated derivatives thereof have a taste bitter. In Chapter 5 attempts are made to palliated this bitter taste by appending a galactosyl moiety to DNJ. Aside from potentially masking the bitter taste this modification will also help to direct the inhibitors to the colon were they will be processed by lactase. Cholesteryl-_-glucoside and cholesteryl-_ -glucoside, the synthesis of which is described in Chapter 6, will be used as as internal standards to get a better insight in the biosynthesis of the potentially neurotoxic steryl-glucosides, which are potentially linked to a high level of glycosylceramide. Chapter 7 summarizes the research described in chapters 2 to 6 and future prospects based on these results are presented. Show less
This study examines the ‘descriptions of cities’ or ‘urban historical topographies’ that were published in the seventeenth-century Dutch Republic. Its questions are: What are the conceptual... Show moreThis study examines the ‘descriptions of cities’ or ‘urban historical topographies’ that were published in the seventeenth-century Dutch Republic. Its questions are: What are the conceptual foundations of the genre? What are the underlying principles that determine the topics that the authors choose and how they approached them? In the chapter-length introduction the genre is defined and an overview is given of the urban topographies published before 1700, situating them in their political and social context. Aspects of production and reception, belonging to the field of book history, are also discussed. An answer to the study’s main questions is attempted in six chapters. Chapters 2-5 discuss the four most important disciplines that influenced the genre: chorography, encomiastic literature, travel methods, and antiquarian research. Two concluding chapters present two case studies, focussing on the cities of Delft and Leiden in the province of Holland. The first shows how these disciplines converged in urban historical topographies. The second situates them in an international context. Show less
This thesis aimed to evaluate the importance of combined pharmacological and mechanical adjunctive therapies for optimization of outcomes of primary percutaneous coronary intervention (PPCI) in the... Show moreThis thesis aimed to evaluate the importance of combined pharmacological and mechanical adjunctive therapies for optimization of outcomes of primary percutaneous coronary intervention (PPCI) in the setting of ST-elevation myocardial infarction (STEMI), and to assess the predictors of large thrombus burden among STEMI patients and to what extent that would influence the outcomes and the pre-hospital triage of these patients. Furthermore, a special focus was granted on the clinical performance of biodegradable-polymer drug eluting stents (DES) comparing the incidence of definite stent thrombosis (DST) and target lesion revascularization (TLR); a) between biodegradable-polymer biolimus, sirolimus and paclitaxel DES, and b) between biodegradable-polymer DES and permanent polymer DES. We also discussed the recently emerging drugs for coronary artery disease, with special focus on antiplatelets, antithrombotics and anti dyslipidemics. Finally, we provided an overview of post-stenting problems of in-stent restenosis and late stent malapposition. Show less
Depression involves multiple mental problems, including low mood, inability to experience pleasure and emotional, cognitive and behavioral problems. It has a lifetime prevalence of ~15% in the... Show moreDepression involves multiple mental problems, including low mood, inability to experience pleasure and emotional, cognitive and behavioral problems. It has a lifetime prevalence of ~15% in the Dutch population, striking women twice as often as men. The disorder often comprises persisting disturbances in the neuroendocrine stress system, the hypothalamic- pituitary-adrenal (HPA) axis, including disregulation of its end-hormone cortisol. Cortisol normally stimulates emotional, cognitive and behavioral processes in order to cope with a stressor and promotes recovery, learning and memory. This thesis describes the identification of a specific genetic variant of the mineralocorticoid receptor (MR), one of the two receptors for cortisol, which protects against depression. MR transcript expression was found to be lower in postmortem limbic brain regions of depressed patients compared to non-depressed subjects. In addition, a specific and common MR gene variant was identified that results in higher MR expression in vitro. This same variant was found to associate with personality characteristics that predict the risk of depression later in life and with a lower risk of depression itself. All associations were found only in women and not in men. To conclude, the MR is an important determinant of resilience; increased MR expression seems to be protective against depression. Show less
