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
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 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
Johannes Drusius (1550-1616) spent a large part of his life as professor of Oriental languages at the university of Franeker, namely from 1585 to 1616. He was a philologist whose works were... Show moreJohannes Drusius (1550-1616) spent a large part of his life as professor of Oriental languages at the university of Franeker, namely from 1585 to 1616. He was a philologist whose works were reprinted far into the seventeenth, and even in the early eighteenth century. Drusius stimulated research by Christian scholars in the northern Netherlands into Jewish writings. His scholarship in Hebrew and in Jewish works played a vital role in the development of the pedagogical ideal of humanist education with philological stamp. A prominent feature of Drusius' work is his study of Hebrew and Jewish sources for the benefit of explaining passages in the books of the Bible. This research paper constitutes an analysis of Drusius' New Testament commentaries. Chapter one offers a historical sketch of Christian Hebraist studies and in doing so gives a contextualization of Drusius' labours. Chapter two comprises a biography of Drusius. Chapter three clarifies the genre of the 'annotationes', as the contents of Drusius' commentaries consist mainly in philological notes. In chapter four are Drusius' New Testament commentaries discussed. Chapter five is devoted to the relationship between philology and divinity as Drusius saw this. Show less
De Europese aal blijkt bij uitstek een langeafstandsspecialist te zijn. Dit is gebleken uit zwemtesten in 22 zwemtunnels. Het kost schieralen slechts 40% van de vetreserves om de 5500-km naar de... Show moreDe Europese aal blijkt bij uitstek een langeafstandsspecialist te zijn. Dit is gebleken uit zwemtesten in 22 zwemtunnels. Het kost schieralen slechts 40% van de vetreserves om de 5500-km naar de paaigronden in de Sargassozee te overbruggen, mogelijk zelfs in slechts drie-en-een-halve maand. Niet alleen dienen vetten als brandstof, ze zijn ook essentieel als energievoorraad voor de toekomstige larven. Het blijkt nu dat zwemmen de afzetting van de vetten in de eitjes op gang brengt. Door te zwemmen beginnen de eicellen van, vooral oudere, alen te ontwikkelen zodat ze kunnen afpaaien zodra ze in de Sargasso zijn aangekomen. De zwemblaasparasiet beschadigt echter de zwemblaas waardoor geïnfecteerde alen minder efficiënt zwemmen en al het vet waarschijnlijk is verbruikt voordat ze de Sargasso bereiken. Een andere verstorende factor zijn de in het vet opgeloste PCB's, die al in zeer lage doses de vroege ontwikkeling van embryo's onmogelijk blijken te maken. Deze twee factoren lijken een belangrijke oorzaak te zijn in de sterke afname van de wilde populatie. Het feit dat we met zwemmen een natuurlijke 'trigger' hebben gevonden van ontwikkeling van de eicellen en dat we in staat zijn geweest schieralen in gevangenschap tot reproductie te brengen biedt hoop voor toekomstige kweek. Show less
Waar mensen zijn vindt nutriënten-verrijking van het water plaats. In de zomer kunnen algen hierdoor goed groeien. Dode algen en andere resten zakken naar de bodem waarna door rottingsprocessen de... Show moreWaar mensen zijn vindt nutriënten-verrijking van het water plaats. In de zomer kunnen algen hierdoor goed groeien. Dode algen en andere resten zakken naar de bodem waarna door rottingsprocessen de zuurstofconcentratie in het water sterk kan dalen. Het water wordt hierdoor onleefbaar voor vissen en andere organismen. In het Victoriameer in Afrika is het altijd zomer en grote gebieden zijn hier de laatste decennia zuurstofarm geworden. Men kan aannemen dat dit zeer slecht is voor de visstand. Toch blijken Victoriameervissen beter te kunnen overleven dan men dacht. In ons laboratorium in Leiden zagen we drie weken oude Victoriameervisjes (cichlidensoorten) zeer snel konden wennen aan zuurstofarme omstandigheden. Zij bleken zelfs met tien keer minder zuurstof (0,8 mg per liter) net zo hard te groeien als nestgenoten die onder normale omstandigheden leefden. Volwassen vissen gaan dood of overleven dit slechts tijdelijk. Jonge visjes kunnen zo goed overleven omdat zij tot 80% grotere kieuwen krijgen en continue een veel hogere ademactiviteit hebben. De aanleg van deze superkieuwen kost zoveel ruimte dat zelfs hun kop van vorm veranderde. Het bloed dat door de kieuwen stroomt bleek meer en beter zuurstof te kunnen binden terwijl een soort meerdere nieuwe typen hemoglobine bleek te produceren. Dit is een unieke eigenschap die bij andere dieren alleen optreedt bij geboorte of bijvoorbeeld transformaties van water naar land bij amfibieën. Het waterpeil in het Victoriameer was 14.000 jaar geleden extreem laag en mogelijkerwijs heeft een voorouder van deze soort deze truc destijds onder de knie gekregen die in het zuurstofarme water van nu weer van pas komt. Show less
This study of Mamluk metalwork fittings presents a hitherto largely ignored body of Mamluk metalwork objects, i.e. metal-faced doors, doorknockers, window grilles, and window shutters, and aims to... Show moreThis study of Mamluk metalwork fittings presents a hitherto largely ignored body of Mamluk metalwork objects, i.e. metal-faced doors, doorknockers, window grilles, and window shutters, and aims to trace their stylistic and technical development throughout the Mamluk period. In order to establish the uniqueness of Mamluk metalwork fittings, their relationship to pre-Mamluk metalwork traditions and to contemporary designs in other media is analysed. Moreover, the visual relationship between these metalwork artefacts and their immediate architectural context is assessed. Furthermore, attention is directed towards the various metalworking centres such as Cairo, Damascus, and Aleppo and their activities. This study is completed by a catalogue, comprehensively illustrated, comprising a description of embellished metalwork fittings predominantly found in situ in the major cities of the Mamluk realm. Show less
T cells recognize pathogen-derived antigens and are crucial for fighting pathogens such as viruses and bacteria. In addition, T cells are able to recognize and attack certain types of tumors, in... Show moreT cells recognize pathogen-derived antigens and are crucial for fighting pathogens such as viruses and bacteria. In addition, T cells are able to recognize and attack certain types of tumors, in particular virally induced tumors. In this thesis we aimed 1) to obtain more insight into antigen-specific T cell responses and 2) to study how antigen-specific T cell responses can be improved. For the first aim we generated new tools that by enabling the visualization of antigen-specific CD4+ and CD8+ T cells allow the study of the dynamics of antigen-specific T cell responses in time throughout an ongoing immune response (chapter 2). In addition, we developed a novel technique that enables the study of family relationships between different T cell populations. This technique for instance allows us to determine whether two different types of effector T cell populations arise from the same or different pool(s) of na_ve T cells (chapter 5). For the second aim, we analyzed whether antigen-specific T cell responses can be manipulated by providing increased costimulation in the form of constitutive triggering of CD27 (chapter 3) or by generating CD4+ T cells that are modified by the introduction of MHC class I restricted TCRs (chapter 4). Show less
This dissertation investigates A’-dependencies where the dislocated constituent is not transformationally related to the position where it is interpreted. The analysis is carried out within the... Show moreThis dissertation investigates A’-dependencies where the dislocated constituent is not transformationally related to the position where it is interpreted. The analysis is carried out within the Principles & Parameters framework. The first two chapters address relative clauses. Based on a detailed examination of reconstruction, it is argued that German restrictive relatives should be given a Matching Analysis. Chapter three analyzes an alternative to long-distance relativization in German and Dutch where the relative pronoun is governed by the preposition von/van ‘of’ and a resumptive appears instead of a gap in the complement clause. The construction has the hallmarks of an indirect A’-dependency: The external head is interpreted inside the complement clause but cannot be transformationally related to that position. The paradox is resolved by postulating short A’-movement in the matrix clause, operator movement in the complement clause and an ellipsis operation that links the chains. Chapter four analyzes relative clauses in Zurich German. While local relativization is shown to be largely parallel to Standard German, long-distance relativization is reanalyzed in terms of Resumptive Prolepsis. This study is of interest to anyone interested in the syntax of relative clauses, reconstruction, resumption or in the syntax of Standard German, Zurich German and Dutch. Show less
