Dynamic organization of transcription-coupled DNA repair

The aim of the work described in this thesis is to gain more insight in the role of the Cockayne Syndrome A (GSA) and B (CSB) proteins in the process of transcriptioncoupled DNA repair and transcription. Using biochemical analysis and live cell studies we investigated the molecular behavior of both proteins. First, we analyzed the chromatin remodeling activity of CSB. Secondly, using green fluorescent protein (GFP) technology (Chapter 4) and photobleaching we studied (i) the dynamic behavior of CSB in TCR and transcription in living cells, (ii) the kinetics of GSA in TCR and its molecular connection with the CSB protein and (iii) the cellular localization of CSB with respect to other nuclear processes like transcription and mRNA processing

Controlled oleosome extraction to produce a plant-based mayonnaise-like emulsion using solely rapeseed seeds

Oleosomes are oil storage structures in seeds, consisting of triglycerides surrounded by a protein-phospholipid mixed monolayer. They can be extracted aqueously together with other seed components such as proteins and soluble fibers. The co-extracted biomolecules can affect the properties of the extracts. Nevertheless, it is possible to control the electrostatic and hydrophobic interactions between these biomolecules and oleosomes by adjusting the extraction conditions. Hence, our aim was to adjust the extraction conditions in order to recover a natural emulsion with a specific functionality: a plant-based mayonnaise-like product, derived solely from rapeseed seeds. By varying the pH of extraction, the droplet size was customized and by increasing the number of purification steps, the right amount of co-extracted material was removed. A combination of these conditions shifted the rheological properties of the obtained natural emulsion to a range similar to the benchmark mayonnaises. This work shows that it is feasible to produce a plant-based mayonnaise with an oil content ranging from 61.7 g/100g to 72.0 g/100g through a simple and continuous oleosome extraction process by controlling the interactions between oleosomes and co-extracted material.</p

Evidence-based diagnosis and treatment of macrophage activation syndrome in systemic juvenile idiopathic arthritis.

Background Macrophage activation syndrome (MAS) is a severe and potentially lethal complication of several inflammatory diseases but seems particularly linked to systemic juvenile idiopathic arthritis (sJIA). Standardized diagnostic and treatment guidelines for MAS in sJIA are currently lacking. The aim of this systematic literature review was to evaluate currently available literature on diagnostic criteria for MAS in sJIA and provide an overview of possible biomarkers for diagnosis, disease activity and treatment response and recent advances in treatment. Methods A systematic literature search was performed in MEDLINE, EMBASE and Cochrane. 495 papers were identified. Potentially relevant papers were selected by 3 authors after which full text screening was performed. All selected papers were evaluated by at least two independent experts for validity and level of evidence according to EULAR guidelines. Results 27 papers were included: 7 on diagnosis, 9 on biomarkers and 11 on treatment. Systematic review of the literature confirmed that there are no validated diagnostic criteria for MAS in sJIA. The preliminary Ravelli criteria, with the addition of ferritin, performed well in a large retrospective case-control study. Recently, an international consortium lead by PRINTO proposed a new set of diagnostic criteria able to distinguish MAS from active sJIA and/or infection with superior performance. Other promising diagnostic biomarkers potentially distinguish MAS complicating sJIA from primary and virus-associated hemophagocytic lymphohistiocytosis. The highest level of evidence for treatment comes from case-series. High dose corticosteroids with or without cyclosporine A were frequently reported as first-line therapy. From the newer treatment modalities, promising responses have been reported with anakinra. Conclusion MAS in sJIA seems to be diagnosed best by the recently proposed PRINTO criteria, although prospective validation is needed. Novel promising biomarkers for sJIA related MAS are in need of prospective validation as well, and are not widely available yet. Currently, treatment of MAS in sJIA relies more on experience than evidence based medicine. Taking into account the severity of MAS and the scarcity of evidence, early expert consultation is recommended as soon as MAS is suspected

Solitary magnetic perturbations at the ELM onset

Edge localised modes (ELMs) allow maintaining sufficient purity of tokamak H-mode plasmas and thus enable stationary H-mode. On the other hand in a future device ELMs may cause divertor power flux densities far in excess of tolerable material limits. The size of the energy loss per ELM is determined by saturation effects in the non-linear phase of the ELM, which at present is hardly understood. Solitary magnetic perturbations (SMPs) are identified as dominant features in the radial magnetic fluctuations below 100kHz. They are typically observed close (+-0.1ms) to the onset of pedestal erosion. SMPs are field aligned structures rotating in the electron diamagnetic drift direction with perpendicular velocities of about 10km/s. A comparison of perpendicular velocities suggests that the perturbation evoking SMPs is located at or inside the separatrix. Analysis of very pronounced examples showed that the number of peaks per toroidal turn is 1 or 2, which is clearly lower than corresponding numbers in linear stability calculations. In combination with strong peaking of the magnetic signals this results in a solitary appearance resembling modes like palm tree modes, edge snakes or outer modes. This behavior has been quantified as solitariness and correlated to main plasma parameters. SMPs may be considered as a signature of the non-linear ELM-phase originating at the separatrix or further inside. Thus they provide a handle to investigate the transition from linear to non-linear ELM phase. By comparison with data from gas puff imaging processes in the non-linear phase at or inside the separatrix and in the scrape-off-layer (SOL) can be correlated. A connection between the passing of an SMP and the onset of radial filament propagation has been found. Eventually the findings related to SMPs may contribute to a future quantitative understanding of the non-linear ELM evolution.Comment: submitted to Nuclear Fusio

Norovirus genotypes in endemic acute gastroenteritis of infants and children in Finland between 1994 and 2007

Noroviruses are, after rotaviruses, the second most common causative agents of acute gastroenteritis in young children. We studied norovirus genotypes in faecal specimens collected from Finnish children followed-up prospectively in rotavirus vaccine trials. Almost 5000 faecal specimens collected from cases of acute gastroenteritis were examined using reverse transcriptase–PCR. A total of 1172 cases (25% of all acute gastroenteritis) were associated with noroviruses. Of these, 96% were genogroup GII. GII.4 was the most common genotype (46%) throughout the study period but the proportion of this genotype varied in different norovirus epidemic seasons. Additional norovirus genotypes detected were: GII.7 (15%), GII.3 (14%), GII.1 (9%), GII.b (7%), GII.2 (3%), and GI.3 (2%). GII.4 dominated during the following years: 1998–1999 (75%), 2002–2003 (88%) and 2006–2007 (98%) while recombinant genotype GII.b was dominant between 2003 and 2004 (83%). In conclusion, genotypes GII.4 and GIIb have emerged as predominant norovirus genotypes in endemic gastroenteritis affecting young infants and children in Finland

The effect of monovalent (Na+, K+) and divalent (Ca2+, Mg2+) cations on rapeseed oleosome (oil body) extraction and stability at pH 7

Oleosomes are storage vehicles of TAGs in plant seeds. They are protected with a phospholipid-protein monolayer and extracted with alkaline aqueous media; however, pH adjustment intensifies the extraction process. Therefore the aim of this work was to investigate the extraction mechanism of rapeseed oleosomes at pH 7 and at the presence of monovalent and divalent cations (Na+, K+, Mg2+, and Ca+2). The oleosome yield at pH 9.5 was 64 wt%, while the yield at pH 7 with H2O was just 43 wt%. The presence of cations at pH 7, significantly enhanced the yield, with K+ giving the highest yield (64 wt%). The cations affected the oleosome interface and their interactions. The presence of monovalent cations resulted in aggregation and minor coalescence, while divalent cations resulted in extensive coalescence. These results help to understand the interactions of oleosomes in their native matrix and design simple extraction processes at neutral conditions

Fast-ion redistribution and loss due to edge perturbations in the ASDEX Upgrade, DIII-D and KSTAR tokamaks

The impact of edge localized modes (ELMs) and externally applied resonant and non-resonant magnetic perturbations (MPs) on fast-ion confinement/transport have been investigated in the ASDEX Upgrade (AUG), DIII-D and KSTAR tokamaks. Two phases with respect to the ELM cycle can be clearly distinguished in ELM-induced fast-ion losses. Inter-ELM losses are characterized by a coherent modulation of the plasma density around the separatrix while intra-ELM losses appear as well-defined bursts. In high collisionality plasmas with mitigated ELMs, externally applied MPs have little effect on kinetic profiles, including fast-ions, while a strong impact on kinetic profiles is observed in low-collisionality, low q 95 plasmas with resonant and non-resonant MPs. In low-collisionality H-mode plasmas, the large fast-ion filaments observed during ELMs are replaced by a loss of fast-ions with a broad-band frequency and an amplitude of up to an order of magnitude higher than the neutral beam injection prompt loss signal without MPs. A clear synergy in the overall fast-ion transport is observed between MPs and neoclassical tearing modes. Measured fast-ion losses are typically on banana orbits that explore the entire pedestal/scrape-off layer. The fast-ion response to externally applied MPs presented here may be of general interest for the community to better understand the MP field penetration and overall plasma response.Ministerio de Economía y Empresa ((RYC-2011-09152 y ENE2012-31087)Marie Curie (Grant PCIG11-GA-2012-321455)US Department of Energy (DE-FC02-04ER54698, SC-G903402, DE-FG02-04ER54761, DE-AC02-09CH11466 and DE-FG02- 08ER54984)NRF Korea contract 2009-0082012MEST under the KSTAR projec