This thesis centers on the mechanisms of estrogen action and the effects on the development of atherosclerosis. We have focused on the liver as central organ in lipid and glucose metabolism and the... Show moreThis thesis centers on the mechanisms of estrogen action and the effects on the development of atherosclerosis. We have focused on the liver as central organ in lipid and glucose metabolism and the vessel wall as the actual site where the injury occurs. To gain insight in tissue-specific actions of estrogens, we have spent considerable effort to develop tools for liver and blood vessel specific modulation of the estrogen receptor (ER) signaling cascade. The generation, characterization and application of these tools in vitro and in vivo will be described in the different chapters of this thesis. Show less
In this thesis the role of DNA mismatch repair (MMR) in the cellular response to several genotoxic agents is described. We show that MMR plays an important role in the protection against UVC... Show moreIn this thesis the role of DNA mismatch repair (MMR) in the cellular response to several genotoxic agents is described. We show that MMR plays an important role in the protection against UVC-induced mutagenesis in mouse embryonic stem (ES) cells. UVC was shown to induce six times more mutations in mouse ES cells deficient for the mismatch recognition dimer MutSalpha compared to wild type cells. The Hprt mutational spectrum of UVC-induced mutations was similar in MutSalpha-proficient and MutSalpha-deficient mouse ES cells. We subsequently tried to gain insight into the mechanism by which MMR mediates protection against UVC-induced mutagenesis. We found that UVC induces a late S/G2-phase arrest which partially depends on the presence of MutSalpha. The MutSalpha-dependent late S/G2-phase arrest coincided with the appearance of phosphorylated Chk-1 of which the levels were higher in MutSalpha-proficient cells compared to MutSalpha-deficient cells. Importantly, abolishment of the UVC-induced late S/G2-phase arrest in both MutSalpha-proficient and MutSalpha-deficient cells did not result in a smaller difference in mutation induction between both genotypes after UVC treatment. We propose that MMR removes mismatches from UVC-induced compound lesions and that the MutSalpha-induced late S/G2-phase arrest is the result of the appearance of DNA single stranded regions arising during this process of MMR. Show less
Reumatoide arthritis (RA) is een ernstige, chronische ontstekingsziekte van de gewrichten. Hoofdstuk 1 is een introductie in epidemiologische gegevens over RA en factoren van invloed op... Show moreReumatoide arthritis (RA) is een ernstige, chronische ontstekingsziekte van de gewrichten. Hoofdstuk 1 is een introductie in epidemiologische gegevens over RA en factoren van invloed op ziektebeloop. Hoofdstuk 2 bespreekt de voorspellende waarde van anti-CCP antistoffen bij patiënten met nog niet te classificeren artritis voor het ontstaan van RA binnen 3 jaar. Deze antistoffen blijken belangrijke voorspellers te zijn voor het ontwikkelen van RA bij deze groep patiënten en een waardevolle aanvulling voor het vroegtijdig stellen van de diagnose RA. Hoofdstuk 3 onderzoekt de voorspellende waarde van de verdeling van ontstoken gewrichten bij eerste polibezoek op de ernst van röntgenologische schade in de toekomst. Artritis van de grote gewrichten vooral van de knie hangt hiermee samen. Hoofdstuk 4 analyseert volledige klinische remissie bij patiënten met RA. In een RA cohort uit Leiden vertoonde 10% blijvende remissie. Deze patiëntengroep werden gekenmerkt door afwezigheid van antistoffen. Hoofdstuk 5 beschrijft een gen-omgevingsinteractie tussen roken en de aanwezigheid van anti-CCP antistoffen bij patiënten met RA die drager zijn van bepaalde HLA klasse II allelen (de shared epitope allelen). Hoofdstuk 6 is een theorie over de oorzaak van de afgenomen incidentie van RA in de afgelopen decennia door een veranderde genetische samenstelling van de populatie. Show less
In a surveillance study in Jakarta, Indonesia, 88 typhoid and 26 paratyphoid fever patients were identified by blood culture. Risk factors for transmission of typhoid fever were mainly intra... Show moreIn a surveillance study in Jakarta, Indonesia, 88 typhoid and 26 paratyphoid fever patients were identified by blood culture. Risk factors for transmission of typhoid fever were mainly intra-household factors (poor hand-washing hygiene, recent household contacts), whereas paratyphoid was mainly contracted through street food. In an additional study, street vendors observed poorer hand-washing and food-handling hygiene compared to food handlers in restaurants, and had higher bacterial loads in dishwater. Further host factor-studies in (para)typhoid patients revealed that polymorphisms in genes encoding pro-inflammatory cytokines (IFN-_, IL1A/B, IL1R1, TNFRSF1A, CASP1 and CRP) were not associated with susceptibility to typhoid fever, and might therefore at most be associated with severity of disease. An association was found of typhoid fever and a polymorphism in the PARK2/PACRG proteasome-mediated protein degradation pathway through ubiquitination, similar to infection with Mycobacterium leprae. Also an association between genotypes in the Cystic Fibrosis Transmembrane Conductance Regulator (the affected protein in Cystic Fibrosis) and susceptibility to typhoid fever was found, suggesting a decreased adherence potential of S. typhi to intestinal mucosal cells with these polymorphisms. Finally, bacterial characteristics were compared by use of AFLP and biochemical/antibiotic susceptibility profiles, showing very homogeneous S. typhi and S. paratyphi A strains circulating in the study area. Show less
Many cellular processes are studied by biochemical techniques. Usually, this involves experiments where large number of cells are lysed, protein content is subsequently isolated and studied using... Show moreMany cellular processes are studied by biochemical techniques. Usually, this involves experiments where large number of cells are lysed, protein content is subsequently isolated and studied using antibodies to detect changes in protein levels, post-translational modifications, pairing with partner molecules, etcetera. Although informative, these mass population analyses often lack the time resolution to study rapid alterations in protein state, and do not allow the characterisation of highly dynamic processes. Moreover, analysis of millions of cells at once evidently shows the average response in the population of cells, thereby obscuring cell-to-cell variation and the dynamic range of a process. With the availability of microscopic techniques in combination with genetically encoded fluorescent probes, many of these restraints have been overcome. Highly dynamic reactions can now be studied in detail in a relatively easy manner, and in the context of a living cell, hence "single cell biochemistry". In this way, we studied two different cellular processes, antigen presentation and drug resistance in unprecedented detail. Both parts seem at first unrelated, yet are interconnected through the use of similar techniques. Assessment of individual cells using sensitive microscopic measurements, has led to important and detailed understanding of the dynamic processes involved in both topics. Show less
This dissertation centres on the books by Freud that have been published in Dutch during the twentieth century. It is to a great extent due to his books that Freud has established his name in The... Show moreThis dissertation centres on the books by Freud that have been published in Dutch during the twentieth century. It is to a great extent due to his books that Freud has established his name in The Netherlands in cultural, social and scientific respects. Through the publishers activities insight is gained into the reproduction, interpretation and reception of Freud’s work. Translators and editors are also followed by researching their perception of Freud and their principles of translating. Publishing is a complicated process. It has become clear that maintaining a good network was crucial for all the publishers, whereby the publishers functioned as ‘gatekeepers’. They played a defining and central role in the realization of the publications. Attention is also payed to the way in which Freud’s books are published in The Netherlands by researching the ‘paratext’, such as introductions, forewords, jackets texts, notes and glossaries, typography and lay-out. It is possible to deduce the aims of Freud’s publishers from the ‘paratext’; they clarify how Dutch publishers have introduced and presented Freud’s work and which images of Freud this created. The study examines several publishing houses and their publications of Freud. The firm S.C. van Doesburgh introduced Freuds work, the Wereldbibliotheek was responsible for the popularization of Freud’s texts and Uitgeverij Boom for the canonization of Freud’s work.The international developments in Freud publishing and editing are discussed and the study concludes with a number of suggestions for future translations of Freud’s texts. Show less
The current and increasing interest of local, regional and global actors in the region is related, in particular, to the possible reserves of oil and natural gas in the Caspian Sea. After the... Show moreThe current and increasing interest of local, regional and global actors in the region is related, in particular, to the possible reserves of oil and natural gas in the Caspian Sea. After the collapse of the Soviet Union, slumbering ethnic sentiments were unleashed and developed into violent conflicts. Subsequently, weak state structures and tense relations between ethic groups have caused instability, political disagreement, conflicts and economic decline. Furthermore, in addition to local reasons for conflict, the political-strategic and economic importance of the South Caucasus has been ground for (attempts at) involvement in this area by states and organisations, such as Iran, Turkey, Russia, the USA, NATO and the EU. Show less
Surgery is the most effective cancer therapy, followed by radiotherapy. These techniques usually target tumour specific tissue only, unlike most forms of chemotherapy as is best illustrated by the... Show moreSurgery is the most effective cancer therapy, followed by radiotherapy. These techniques usually target tumour specific tissue only, unlike most forms of chemotherapy as is best illustrated by the relatively moderate side effects of such treatments. When the immune system could find and destroy tumour cells, they (and their metastases) would be selectively destroyed without to many side effects as well. But then tumour cells have to be recognized and this requires presentation of tumour specific proteins to the immune system. This process called antigen presentation by the MHC class I molecules is studied here. Chapter 1 and 2 form an introduction to the ubiquitin proteasome system and the MHC class I antigen presentation route, which is operational in most cell types and is involved in presentation of antigens derived from degraded intracellular proteins (of self, tumour or viral origin). Proteins are not randomly degraded, but targeted for degradation by ubiquitin or ubiquitin-like post-translational modifications and subsequently degraded by the major cellular protease, the proteasome. Proteins are not only targeted for degradation because they are old, they may also be targeted for example in a cell cycle specific way or just because they have not been folded correctly during protein synthesis. Further trimming to free amino acids by other proteases follows degradation of cellular proteins by the proteasome. Only a minor pool of peptides that meets the requirements for antigen presentation may circumvent further degradation by binding to proteins involved in MHC class I presentation, like the transporter associated with antigen presentation (TAP), and MHC class I itself. Once the peptide is loaded onto MHC class I, the MHC class I-peptide complex can be transported to the plasma membrane. Here, the peptide is presented to cytotoxic T-cells (CTLs), which can in this way examine the intracellular protein content in their search for foreign content. The first step in antigen presentation by MHC class I is the decoration of target proteins with a degradation signal. The first discovered and best-studied degradation signal is a polymer of ubiquitin proteins. A ubiquitin polymer of more than four ubiquitin proteins can be recognized by the proteasome and subsequently unfolded, de-ubiquitylated and degraded by the proteasome. Free ubiquitin and mono- ubiquitylated proteins are not targets for degradation, but serve other functions. Most studies on ubiquitin have been of biochemical nature, but the introduction of the green fluorescent protein (GFP) allowed the study of ubiquitin behaviour in living cells. It was shown before that a GFP-ubiquitin construct could be stably expressed in human cells. In chapter 4, we have used this chimeric protein to study ubiquitin in living cells under normal cell culture conditions and during proteotoxic cell stress as the result of proteasome inhibition, and heat shock. In untreated cells we were able to confirm previous biochemical experiments showing that a large pool of ubiquitin molecules is coupled to histone 2A and 2B in the nucleus, whereas a small pool of ubiquitin is present as free monomers in both nucleus and cytosol. A third pool of ubiquitin was present in the form of ubiquitin polymers in both the nucleus and the cytosol. Manipulation of the cells with different proteotoxic stress conditions revealed a rapid de-ubiquitylation of the histone-bound ubiquitin pool in favour of poly-ubiquitin chains, which may even reach a size similar to the proteasome complex, which is at least one hundred times bigger as a single ubiquitin molecule. These rapid changes in the ubiquitin equilibrium do not only affect proteasomal degradation, but also induce chromatin condensation and altered gene transcription, thus establishing cross talk between these, at first sight unrelated, cellular processes. Alterations in the UPS are correlated with a variety of human pathologies, like cancer, immunological disorders, inflammation and neurodegenerative diseases. The exact role of the UPS in the pathophysiology of these diseases however, remains poorly understood. Because ubiquitin and the ubiquitin proteasome system are involved in several neurodegenerative diseases like Parkinson__s disease, Alzheimer__s disease and polyglutamine diseases like Huntington__s disease we set out our hypothesis of a sensitive ubiquitin equilibrium in the cell in chapter 5. Besides surgery, radiotherapy is one of the most effective ways of anticancer treatment. The main effects of radiotherapy on cells are induction of double-stranded DNA breaks and the formation of reactive radical species, which may lead to protein modifications like amino acid side-chain oxidation and breakage of di-sulphide bonds. These modifications will hopefully lead to DNA and protein damage, sufficient for cells to enter apoptosis or cell arrest. In chapter 6 we have shown that following exposure to g-irradiation, cell surface MHC class I-peptide complex expression is dose dependently upregulated in two phases. In the first phase of upregulation, proteins are degraded and presented that were directly damaged by the radiation and subsequent radical formation. The second phase is caused by a radiation driven activation of the mTOR pathway, which results in enhanced protein synthesis. This leads to the formation of malformed proteins called rapidly degraded proteins (RDPs) or defective ribosomal products (DRiPs) that are subsequently degraded by the proteasome and presented by MHC class I. The second phase does not only quantitatively alter MHC class I expression, but because of the mTOR pathway-specific protein expression also qualitatively. In addition, proteins may be upregulated to g-irradiation especially DNA repair proteins, resulting in more specific peptides. CTLs directed against these radiation-specific peptides were found in peripheral blood, but appeared in an anergic state. The existence of these CTLs and the expression of radiation-specific peptides may explain the inhibition of distant tumours after local radiotherapy if these CTLs could be activated. This effect is known as the abscopal effect of local radiotherapy. If these CTLs could be activated prior to irradiation in a combination therapy, these could induce a potent immune response against the irradiated cells. We show that prior radiation of a local tumour strongly improves the response to immunotherapy (adoptively transferred CTLs), showing the feasibility of a novel combination therapy: radio-immuno therapy. The majority of MHC class I loaded peptides is derived from cytosolic proteins. But it has been shown that MHC class I also presents peptides derived from extracellular sources like bacteria and proteins from neighbouring cells. This phenomenon is called cross-presentation and many pathways have been postulated to explain how proteins from extracellular sources may intersect with the MHC class I loading machinery. Examples are endosome to cytosol relocation, intercellular peptide transport through gap-junctions, exosomes and ER-phagosome fusion. In chapter 3, we have evaluated the evidence for and against the ER-phagosome theory and concluded that cross-presentation via fusion of phagosomes with the ER is very inefficient if at all possible. Our evaluation of the ER-phagosome theory was a commentary on a study by Touret et al, 2005. This study attempted to validate previous results leading to the ER-phagosome fusion theory, but failed to do so. We have also tried to show ER-phagosomal fusion in dendritic cells, but the best near-fusion event of the ER we could find was a close encounter of ribosome containing ER membranes with a mitochondrion. Also our calculations on the odds of presentation of phagosome-derived peptides were not in favour of antigen presentation via ER-phagosome fusion events. We conclude that cross-presentation to support vaccination should find a different route. Show less
The present study comprises a classification and analysis of the syntax of the non-verbal clause in Qumran Hebrew, i.e. the linguistic variety (or varieties) found in the so-called Dead Sea Scrolls... Show moreThe present study comprises a classification and analysis of the syntax of the non-verbal clause in Qumran Hebrew, i.e. the linguistic variety (or varieties) found in the so-called Dead Sea Scrolls. The corpus consists of the non-biblical texts written in Hebrew; biblical texts and texts written in Aramaic are excluded. Chapter 1, ‘Introduction’ discusses methodological problems (approach, description) and provides an overview of non-verbal clause patters in variety of Semitic languages. Chapter 2, ‘A survey of previous research’, summarises the results of earlier research into specifically Biblical, Mishnaic and Qumran Hebrew. Chapter 3, ‘The non-verbal clause in Qumran Hebrew’ is the core of the present work, which offers an analysis of the syntax of the non-verbal clause (including the existential clause) in Qumran Hebrew. Chapter 4 contains the conclusions. A bibliography, a Dutch summary and a Curriculum Vitae are appended. Show less
Efficient execution of large-scale application codes is a primary requirement in many cases. High efficiency can only be achieved by utilizing architecture-independent efficient algorithms and... Show moreEfficient execution of large-scale application codes is a primary requirement in many cases. High efficiency can only be achieved by utilizing architecture-independent efficient algorithms and exploiting specific architecture-dependent characteristics of a given computer architecture. However, platform specific versions of source code must be avoided to limit development and maintenance complexity. Usually, the problem can be formulated on an abstract level (mathematical equations, English). At that level, the problem is completely known, and there is no reference to the hardware on which the problem will be solved. Unfortunately, often the advantages of a high level of abstraction are overshadowed by a loss of performance compared to handwritten code. Therefore, a problem-specific code generator, called Ctadel, has been developed in order to exploit architecture-independent and dependent optimizations. We show how to extend Ctadel with more advanced numerical techniques and a interfaces to numerical libraries. A number of numerical models from Hirlam, a numerical weather prediction application in use by a number of meteorological institutes like the Dutch royal meteorological institute (KNMI) where specified using our specification language. We compared the performance of the generated program code with hand-written code. In most case, the code generated by Ctadel performs as well or even better than the hand-written code. Show less
Under the influence of increasing globalisation the creation and development of technology-based entrepreneurial firms is considered a prevalent means to fuel economic growth and prevent further... Show moreUnder the influence of increasing globalisation the creation and development of technology-based entrepreneurial firms is considered a prevalent means to fuel economic growth and prevent further unemployment, especially in Western European economies. This dissertation denotes the process of new venture growth employing a dynamic capabilities framework. In this context, dynamic capabilities are a company's ability to adapt its organisational setup when growing. The study comprises 44 new and high-growth ventures in the Munich region that are observed over a period of almost 6 years on average. Thus, the research design considers the longitudinal and dynamic character of the entrepreneurial growth process. The findings of this empirical research suggest that the evolution of dynamic capabilities plays a major role in the growth of technology-based new ventures. Firms that are not able to develop certain functional skills jeopardise initial performance. However, not all capabilities fuel organisational growth from the start. Thus, management teams should carefully prioritise to deploy their scarce resources effectively. Reflecting on the results of this study the sequence of capability evolution also has a significant impact on new venture performance. Companies following a "logical" sequence show higher growth rates than other new ventures in their early days. Show less
This thesis investigated the association between several genetic factors and autoantibodies and the development of undifferentiated arthritis (UA) and rheumatoid arthritits (RA). Second, this... Show moreThis thesis investigated the association between several genetic factors and autoantibodies and the development of undifferentiated arthritis (UA) and rheumatoid arthritits (RA). Second, this thesis described a prediction model that estimates the chance to progress from UA to RA. The most important genetic risk factor for RA are the HLA-Class II alleles that encode for a common amino acid sequence, called the ‘Shared Epitope’. Investigating the progression to RA from UA revealed that the HLA-Shared Epitope alleles are not primarily a risk factor for RA but for the presence of anti-CCP antibodies, that are known to be specific for RA. Smoking in the presence of HLA-Shared Epitope alleles particularly increased the risk on anti-CCP-positive RA.. The HLA-DR3 alleles were associated with anti-CCP-negative RA. The presence of HLA-alleles encoding for D70ERAA correlated with a lower risk on RA and a less severe disease course. The presence of the PTPTN22 T-allele conferred an increased risk for both UA and RA. The knowledge on risk factors for RA-development was translated in a model that estimates the chance to progress to RA in patients that present with UA by using 9 clinical variables. The discriminative ability was high and this model allows individualized treatment decisions in UA. Show less
The research in this thesis comprises two separate topics: single-molecule spectroscopy and resonant Raman spectroscopy. The first part concerns single-molecule (SM) spectroscopy on polyethylene ... Show moreThe research in this thesis comprises two separate topics: single-molecule spectroscopy and resonant Raman spectroscopy. The first part concerns single-molecule (SM) spectroscopy on polyethylene (PE) films. Ultra thin (200 nm) films of pure high density PE were produced by spincoating. By determining the position (accuracy 10 nm) and in-plane orientation (acc. 5 deg.) of single 2.3,8.9-dibenzanthanthrene (DBATT) guest molecules, by means of SM microscopy and spectroscopy respectively, we demonstrated that these thin PE films have a shish-kebab morphology, instead of the spherulitic morphology common in thicker PE films. We have also investigated the alignment process of individual quest chromophores by stretching thicker (50 um), low density PE films. Using SM spectroscopy, we have shown that individual guest chromophores are not better aligned along the stretch direction, as draw ratio increases. Instead alignment occurs suddenly, due to the destruction and (oriented) reformation of local crystalline regions and subsequent adsorption of chromophores. Each chromophore's orientation is determined by specific interactions with the oriented PE crystal surface. The second part of this thesis concerns a quantum-chemical analysis of the resonant Raman spectrum of the carotenoid spheroidene reconstituted in the photosynthetic reaction center (RC) of Rhodobacter sphaeroides. Our analysis demonstrates that spheroidene can adopt at least two cis forms in the RC. One of these has been conclusively shown to be the 15,15'-cis structure. Show less
The dissertation analyzes the changing relations between political leadership, sharia and ulama in Tunisia in the nineteenth century. The ideal of an egalitarian society that, as once in Medina... Show moreThe dissertation analyzes the changing relations between political leadership, sharia and ulama in Tunisia in the nineteenth century. The ideal of an egalitarian society that, as once in Medina under the Prophet, lived solely by God's law, has remained an important norm in Muslim society ever since. Meanwhile, in the following centuries, Islam proved to be able to live in harmony with almost absolute political leadership that promulgated its own discrete laws, sometimes even deviating from sharia legislation. This discrepancy between the ideal of an all encompassing sharia and the reality of day to day government had, however, to be bridged. The ruler required the approbation of the ulama, whose fatwas gave his actions a theological basis, establishing a synthesis between doctrine and praxis: they served as mechanisms of legitimization. My study highlights three theological discussions accommodating political leadership in nineteenth-century' Tunisia. I demonstrate that, contrary to characteristics attributed to Islamic law today, the Tunisian muftis did not view the sharia as a rigid and unchangeable entity, but as a law open to new interpretations to serve their Bey. Under the influence of European pressure these mechanisms of legitimization underwent far-reaching changes in the sixties of the nineteenth century. Show less
Worrall, J.A.R.; Machczynski, M.C.; Keijser, B.J.F.; Rocco, G. di; Ceola, S.; Ubbink, M.; ... ; Canters, G.W. 2006
In society there is a constant urge to improve existing devices and the level of success is perhaps the easiest to observe in the world of electronic devices. The complexity, functionality and... Show moreIn society there is a constant urge to improve existing devices and the level of success is perhaps the easiest to observe in the world of electronic devices. The complexity, functionality and reliability of these machines has increased enormously, but it approaches its limits. A new giant step which will provide the space for further development is the concept of molecular electronics where organic molecules and their natural characteristics are used as the functional units. The research presented in this thesis is a small part of the large effort which the scientific community puts nowadays into this goal. The system under the investigation is molecular bridge where the molecule is hydrogen or CO or acetylene or benzene. We characterise junctions by point contact spectroscopy and can address different modes of oscillation by following stretching dependence of vibration energy. Show less
The main theme of this thesis is the catalytic oxidation of CO, which we have investigated on several model catalyst surfaces at atmospheric pressures and elevated temperatures with the combination... Show moreThe main theme of this thesis is the catalytic oxidation of CO, which we have investigated on several model catalyst surfaces at atmospheric pressures and elevated temperatures with the combination of Scanning Tunneling Microscopy and Mass Spectrometry.The study of CO oxidation on low-index and vicinal palladium surfaces has shown that when exposed to ambient pressures of oxygen at elevated temperature, these surfaces oxidize irrespective of their orientation. In this pressure regime the oxides were shown to have a higher reactivity than the metallic surfaces.In a certain window of partial pressure combinations of O2 and CO reaction rate oscillations were observed on Pd(100) and on its vicinal surface Pd(1.1.17). ). CO adsorption on Pt(111) was found to lead to the formation of a regular overlayer structure, identified as (√19 x √19) R23.4°-13CO. The stability of this structure under different reaction conditions was discussed. These results were further used to illustrate the importance of temperature in a catalytic system.Spectacularly high conversion rates could be achieved during CO oxidation at atmospheric pressure on metallic Pt(100) surface. Show less
