180 research outputs found
Multiplexed proteomics mapping of yeast RNA polymerase II and III allows near-complete sequence coverage and reveals several novel phosphorylation sites.
No full textThe multisubunit RNA polymerases (Pols) II and III synthesize mainly eukaryotic mRNAs and tRNAs, respectively. Pol II and Pol III are protein complexes consisting of 12 and 17 subunits. Here we analyzed both yeast Pol II and Pol III by multiplexed mass spectrometric analysis using various proteases and both collision induced and electron transfer dissociation. The cumulative data obtained from using the various proteases (trypsin, chymotrypsin, Glu-C and Lys-C) and the two peptide fragmentation approaches allowed us to map nearly the complete sequences of all constituents of both Pol II and III. Notably, chymotrypsin behaved equally well as and in certain circumstances better than trypsin in the context of protein coverage. Although the available high resolution structures have exposed extensive mechanistic insights into transcription, the role of post-translational modification in these processes has been addressed to a lesser extent. In our analysis of Pol II and III we detected 19 phosphorylation sites, of which 12 have not been previously reported. Identified phosphosites were mapped on the Pol II structure which provided indications that they might play a role in regulating the conformation of the clamp region and, as a consequence, interaction of Pol II with nucleic acids. The described multiplexed proteomics approach is generic and reveals that it is possible to map a protein complex to near completion while applying less than 5 mug (approximately 10 pmol) of total starting material
Computational proteomics: from numbers to biology
No full textThe field of biological research is increasingly trying to understand the complex processes that are too small to observe by eye, even when using a microscope. The real action is taking place at the molecular level; therefore, the only way to investigate this is to use molecular tools. Modern techniques allow studying all proteins in a sample, and the prevailing tool is mass spectrometry based proteomics. As a high-throughput technique, computational analysis is indispensable. In this thesis, we describe several aspects of the treatment of proteomics data using in-house developed tools, and the analysis of several biological experiments. In a first example to illustrate how we used mass spectrometry to investigate biological problems, we investigated the evolution of tyrosine phosphorylation, which possibly arose simultaneously with multicellularity. To investigate this, the placozoan Trichoplax adhaerens was analysed, which is arguably the most primitive animal. We observed several tyrosine kinases in the genome sequence, and phosphoproteomics analysis revealed an extraordinary amount of tyrosine phosphorylation events compared to modern animals. In a second example, we simultaneously analysed RNA, DNA and proteins in a study of a single organ, the rat liver. We compared two different rat strains, the Brown Norwegian (BN) rat, and a variant exhibiting spontaneous hypertension (SHR). Through these measurements we found a differentially regulated rat homolog of a gene that is linked to hypertension in human, CYP17A1, both at the RNA and at the proteome level. The DNA sequence showed a polymorphism in the gene promoter, indicating that a single point mutation may be responsible for the mis-regulation of this gene and protein
A Decision-Support System based on Real Time Control and Data Assimilation: A test case in Twentekanalen
No full textThe integration of forecasting and decision-making in real-time Decision-Support Systems (DSS) provides a powerful tool to operators of water resources systems for evaluating the future control of hydraulic structures. Decisions may be supported by presenting information about predicted disturbances, e.g. inflows into the water system, enabling the operator to try out future trajectories of structure control, or suggesting an optimum control based on predictive controllers. Ongoing work is undertaken under the programme Flood Control 2015 (FC2015) with respect to the management of flood events. This MSc thesis research was supervised jointly by the Operational Water Management research group of Delft University of Technology and the research institute Deltares. The aim of the MSc project is the transfer and extension of real-time DSS knowledge and techniques to a typical Dutch canal system such as Twentekanalen using simulation tools in development at Deltares. The main research objective is to assess the potential of DSS in this context and to investigate and verify a robust concept for applying Model Predictive Control on canal systems, taking into account missing or wrong data by applying Data Assimilation techniques. The main system characteristics and relevant processes of the Twentekanalen system are the following: \u95 3 Canals connected by locks in which the water level needs to be controlled. \u95 The water level is chiefly governed by the operation of locks, which need to turn in order for ships to pass, discharging a large quantity of water each time in comparison to other water flows in the system. Measurements of water level and flows at the locks are relatively complete. \u95 The water level is regulated by pumps and discharge structures at the locks \u95 Other water flows that occur in the system are lateral inflow and outflow. The measurements of these flows are relatively incomplete. At the start of the research a set of tools was available at Deltares. FEWS, a data management system, and RTC Tools, a reservoir routing model in development which was later extended with Data Assimilation capabilities. Near the end of the research a detailed model of the system in Sobek, a 1D and 2D water flow model, became available. A model framework has been designed to assess the potential of applying MPC and DA in a DSS for such a system. The incremental design and verification of this model framework has been the core of this research. The novel research is the addition of Data Assimilation techniques to Model Predictive Control. In order to show the added value of DA and verify its implementation a verification approach is needed to address the other components in the framework as well. The first method taken to achieve this was to set-up the MPC for Twentekanalen and integrate it into Delft-FEWS in hindcast mode assuming a perfect forecast. When the data set was made available it became clear that it contained large water balance errors. Adding DA showed improvements in the forecast, but while using realistic values for the DA, the forecasts were still far from accurate. By creating a workaround in the DA module it was shown that especially the Eefde-Delden reach had a large balance error that did not have a high correlation with the known lateral flows. Considering the low quality of the data set it was decided to expand the scope of the research and replace the data set by an accurate hydraulic model that became available near the end of this research. This model still uses measurements from the Twentekanalen system as input, but with internal controllers to regulate the pump and spill structures the water balance is maintained. With an extra expansion to inject known errors in the system, a thorough investigation of the effects of Data Assimilation and Model Predictive Control can be executed. First results from this expanded approach show promising results, but because of practical implementation issues of conflicting software modules, the full results will not be available within this research. Conclusions: From a theoretical point of view DA has a lot of potential. State updating solves an important issue of real time control; keeping the model state as close as possible to the real system state. Model training by parameter updating can be a good way to increase model forecasting performance. Online Parameter Updating can be very effective in systems were a high correlation occurs between measurements and unmeasured processes. These elements will make the model more robust, it can adapt to changing conditions. This also provides the model developer with interesting feedback on the workings of the modeled water system. From a practical point of view DA has shown improvements in the performance of the DSS as designed within this thesis project. But because of the large errors in the measurements it is difficult to translate these improvements to the effects in other systems. Implementation of the designed model framework gives a more satisfactory answer to that question. Recommendations have been made for improvements of the RTC Tools module, the development of prediction modules for the Twentekanalen system and further research using the developed framework with the models, scripts and programs written for this research. Most importantly getting predictions and real-time measurements on lock turning in the Twentekanalen system, and increasing the flexibility of model design in RTC Tools.Water ResourcesWatermanagementCivil Engineering and Geoscience
Visualising the status of building elements in construction projects: An approach to using BIM4D techniques to visualise infield status of building elements
No full textCivil Engineering and GeosciencesStructural EngineeringConstruction Management and Engineerin
Improvement and scale enlargement of the inflatable rubber barrier concept: A case study applicable to the Bolivar Roads barrier, Texas, USA
No full textAn ambition is that in the near future more inflatable dams can be applied as storm surge barriers. Hence, the main objective of this study is to investigate the applicability of rubber storm surge barriers at larger scales than currently applied. To achieve this objective the inflatable barrier concept (inflatable barriers applied as storm surge barriers) is further improved. The barrier of Ramspol in the Netherlands is taken as a reference point for this study in order to improve the inflatable barrier concept. Based on the knowledge and experience derived from the Ramspol barrier, the following issues should be addressed in order to make further improvements to the inflatable barrier concept: \u95 Increase the reliability of inflatable dams; \u95 Gain more knowledge about the limits of the dimensions of inflatable dams; \u95 Improve the geometry of abutments; \u95 Improve the storage of the sheet of the inflatable dam. In this report two inflatable barrier designs are presented for the case study: Bolivar Roads, Galveston Bay, Texas, USA. This location requires a very large barrier due to its large width (± 3000 m) and water depth (15 m). Design 1 This design is based on Ramspol, but has been improved and scaled up to allow the application for the location Bolivar Roads. The inflatable dam of Bolivar Roads has the shape of an ellipsoid above the abutment and the middle part of the dam is like a ‘normally’ shaped inflatable dam. Design 2 The second design is innovative and based on large scale conditions. Since a 100% closure is not demanded for the Bolivar Roads barrier application, an inflatable dam without (a connection with) abutments was chosen due to the favourable force transfer. Each inflatable dam has the shape of an ellipsoid in the end parts, and a ‘normally’ shaped inflatable dam in the middle part. In both designs the previously mentioned issues were addressed. The first two issues (reliability and limits of the dimensions) are identical for both designs, whereas the last two (geometry of abutments and storage of sheet) are not. The most important measure for increasing the reliability of the barrier is to chain multiple smaller length (100 m) are not desired, because a collapse of a long dam can cause flooding downstream. More knowledge about the limits of the dimensions of an inflatable rubber barrier is obtained by scale enlargement of the Ramspol barrier (2.3 times higher). Proven by this case study it appears that large dimensions (height: 19 m) are feasible for inflatable barriers. In both designs folds and peak stresses in the sheet are reduced significant compared to Ramspol. However, design 2 results in even more reduction of folds and peak stresses in the sheet than design 1, due to the absence of the connection with the abutments. Also design 2 has a higher reliability due to the larger number of inflatable dams. Therefore, design 2 was the chosen option for the final design of the barrier of Bolivar Roads.Hydraulic EngineeringStructural EngineeringCivil Engineering and Geoscience
Enhancing Fiber Direction Estimation from Electrograms: A Comparative Study and Method Improvement for Clinical and Research Applications
No full textFor the heart to pump blood throughout the body, electrical impulses that trigger the cellular contraction must be generated and spread through the myocardial tissue. These signals propagate faster along the longitudinal cardiac fiber direction than the transverse direction, conferring the heart with anisotropic conduction properties. Therefore, the arrangement of the fibers within the tissue governs the impulse propagation. Given the variability of the fiber direction across the heart and between patients, incorporating it into electrophysiological models would enhance our understanding of the mechanisms and progression of different heart conditions, such as atrial fibrillation (AF). The study of this common cardiac arrhythmia relies on analyzing electrical recordings of the heart, known as electrograms (EGMs), which, if integrated with the patient’s fiber architecture into cardiac models, can enable effective personalized treatment. Over the years, researchers have proposed different approaches to estimate the fiber direction from EGMs. However, these methods have been evaluated in different, usually simplistic, cardiac tissue models, making their comparison, and therefore selection of the most accurate approach for clinical and research applications, challenging.The current study aims to identify the best fiber direction estimation method under consistent and realistic conditions. To achieve this goal, synthetic EGMs and local activation time (LAT) maps were generated from 2D and 3D monodomain models that mimicked the muscle bundle, atrial bilayer, and ventricular transmural fiber rotation structures. A comparison analysis of existing fiber direction estimation methods, first as described by their authors and then standardized to have the same spatial resolution, showed the superior performance of the techniques based on fitting an ellipse to local conduction velocity or conduction slowness vectors from a whole LAT map. The estimation accuracy of these methods can be further improved by increasing the number of vectors to which the ellipse is fitted. Nonetheless, given the influence of underlying layers in the epicardial recordings, the estimation error increases in the tissue models where fibers in the epicardial and endocardial layers run perpendicularly. The effect on the estimate of such architecture, characteristic of the inferior side of the right atria and the ventricles, can be accounted for by combining epicardial electrical recordings obtained after pacing either in the endocardium or the epicardium. Although a preliminary assessment of the estimation methods was carried out with human EGMs, future studies should focus on validating the methods in a controlled experimental framework and refining them for more localized fiber direction estimation. All in all, the automation of the techniques and their integration into electrophysiological models brings us a step closer to creating valuable clinical tools for diagnosing and treating electropathologies.Biomedical Engineerin
Computational proteomics: from numbers to biology
No full textThe field of biological research is increasingly trying to understand the complex processes that are too small to observe by eye, even when using a microscope. The real action is taking place at the molecular level; therefore, the only way to investigate this is to use molecular tools. Modern techniques allow studying all proteins in a sample, and the prevailing tool is mass spectrometry based proteomics. As a high-throughput technique, computational analysis is indispensable. In this thesis, we describe several aspects of the treatment of proteomics data using in-house developed tools, and the analysis of several biological experiments. In a first example to illustrate how we used mass spectrometry to investigate biological problems, we investigated the evolution of tyrosine phosphorylation, which possibly arose simultaneously with multicellularity. To investigate this, the placozoan Trichoplax adhaerens was analysed, which is arguably the most primitive animal. We observed several tyrosine kinases in the genome sequence, and phosphoproteomics analysis revealed an extraordinary amount of tyrosine phosphorylation events compared to modern animals. In a second example, we simultaneously analysed RNA, DNA and proteins in a study of a single organ, the rat liver. We compared two different rat strains, the Brown Norwegian (BN) rat, and a variant exhibiting spontaneous hypertension (SHR). Through these measurements we found a differentially regulated rat homolog of a gene that is linked to hypertension in human, CYP17A1, both at the RNA and at the proteome level. The DNA sequence showed a polymorphism in the gene promoter, indicating that a single point mutation may be responsible for the mis-regulation of this gene and protein
Proefproject Amsterdam-Rijnkanaal
No full textHet proefproject Amsterdam-Rijnkanaal (ARK) is een onderdeel van het project Veiligheid Vervoer over Water (VVW). De vraagstelling van het proefproject is: "Welke maatregelen moeten genomen worden om de veiligheid op en om het ARK te waarborgen, rekening houdende met te verwachten ontwikkelingen in de komende 10 jaar?" Hiervoor is een afwegingskader opgesteld. Deze bestaat uit: - Risiconormen; - Risicoberekeningen; - Schattingen van effecten van maatregelen. M.b.t. de huidige veiligheid zijn de volgende conclusies getrokken: - Huidige risico hoger dan de grenswaarde t.p.v. woonhuizen in Maarssen, woonwijken in Breukelen en Utrecht en industrieterreinen in Amsterdam, Diemen en Utrecht. Bepalend hiervoor is het vervoer van giftige vloeistoffen in enkelwandige tankers, met name benzeen, tolueen, styreen en VN1992. - Risico hoger dan de streefwaarde t.p.v. woonhuizen in Diemen, Driemond, Nigtevecht, Maarssenbroek, Wijk bij Duurstede en Rijswijk en industrieterreinen in Weesp, Nigtevecht, Breukelen, Maarssenbroek, Wijk bij Duurstede en Tiel. Bepalend hiervoor is het vervoer van ammoniak in druktankers. De toekomstige ontwikkelingen leiden tot een verhoging van de risico. Uit het onderzoek volgen de volgende aanbevolen maatregelen: 1. Instelling van een Verkeersbegeleidend Systeem Verwacht effect: 7% minder ongevallen en een verbetering van de verkeersafwikkeling Kosten op jaarbasis: ca. f. 2.000.000 2. Technische maatregelen: -Marifoonverplichting -Verplichte noodstroomvoorziening -Jaarlijkse veiligheidskeuring Verwacht effect: ca. 7% minder ongevallen Kosten op jaarbasis: f. 150.500 3. Giftige vloeistoffen, met name VN1992, tolueen en styreen in dubbelwandige tanksschepen vervoeren of omleiden over zee. Verwacht effect: oplossing aandachtspunten IR 4. T.a.v. ammoniakvervoer: alles gekoeld vervoeren in drukbestendige tankers en omleiden over zee, voor zover mogelijk. Kosten op jaarbasis: f. 94.500 5. Voor nieuwbou een zonering hanteren van min. 30 m ten noorden van de splitsing met het Lekkanaal, 20 m voor het Betuwepad tussen Lek en Waal en 10 m voor de rest van het kanaal. 6. Instellen van een minimumsnelheid van 8 km/h en strenger controleren van de huidige maximumsnelheid. Verwacht effect bij volledige naleving: ca. 10% minder ongevallen 7. Randverschijnselen: -Verlichting als signalering waar gespuid wordt (kosten op jaarbasis: ca. f. 2000) -Bij vergunningaanvragen meer letten op spuisnelheid en verlichtingssterkte 8. Toegestane breedte verhogen van 11,4 m naar 22,8 m. Geldt formeel nog niet voor alle schepen. 9. Bestaande ligplaatsen nabij de Pr. Beatrixsluis en de Pr. Irenesluis bestemmen tot wachtplaatsen met aparte wachtplaatsen voor schepen met gevaarlijke stoffen. 10. Aan beide zijden van de kruising met de Lek een bord plaatsen waarop de stroomsnelheid op de rivier wordt vermeld, met automatische berekening en presentatie van de informatie. Kosten: enkele tienduizenden guldens 11. Het verplaatsen van de ligplaatsen Breukelen en Utrecht-Kanaleneiland naar een andere locatie langs het kanaal. Verwacht effect: ca. 50% vermindering van het aantal ongevallen op die plaatsen. Kosten op jaarbasis: f. 178.000 (Breukelen) + f. 400.000 (Kanaleneiland). 12. Beter gedrag bij mist: zonder radar niet uitvaren danwel de eerste veilige ligplaats kiezen. Verwacht effect: 1 à 2% minder ongevallen Kosten op jaarbasis: f. 167.000 13. Opleiding: -Radardiploma voor degene die het radarbeeld interpreteert; -Her- en bijscholingscursussen; -Simulatortrainingen in de opleiding Verwacht effect: 6% minder ongevallen Kosten op jaarbasis: f. 144.000Veiligheid Vervoer over Water (VVW
Groundwater Quality in Curaçao: A hydrochemical multi-annual assessment (1977-2021) of a Caribbean island
No full textFor this thesis a hydrochemical groundwater survey was carried out on the Caribbean island of Curaçao in 2020 as part of the NWO SEALINK project. In order to be well-adapted against anthropogenic and natural pressures, Curaçao needs representative data, yet thorough hydrochemical datasets were only sparsely collected in the wet seasons of 1977 and 1992. The aim of this thesis was to determine the current chemical state of the groundwater and analyze for long-term pollution trends with an extended database spanning four decades, also including data that was collected in another fieldwork campaign in 2021.NWO SEALINKCivil Engineering | Environmental Engineerin
The underlying processes of evaporative changes: within the transition period in the Miombo Woodlands, Mpika, Zambia in 2018
No full textThe Miombo woodlands are characterized by a transition period which is defined as the dry period in which grasses wither, trees shed and flush their leaves a few weeks before the rainy season. It is difficult to measure evaporation, due to the influence of the plant water storage on the water availability during the dry season. The seasonal variation in the plant water storage makes it even harder, as the time lag between the plant water storage and the terrestrial groundwater storage varies between the 0 to 90 days depending on the vegetation density. (Tian et al., 2018). It is unclear why the trees prefer this early flushing strategy and what is triggering the shedding of old leaves and flushing of new leaves. It is difficult to remotely sense the variation during this period. In this report, the outputs of several evaporation products and the vegetation indices are studied and compared to see how models follow the transition period. Three models, that are chosen for the comparison use different methods to indirectly calculate the evaporation flux. The first model is the Surface Energy Balance System (SEBS), which is based on the Surface Energy Balance as the name suggests and calculates the evaporation through land-atmosphere relationships. The second model is the Global Land Evaporation Amsterdam Model (GLEAM); this model uses the water balance model to calculate the water stress factor and in return the actual evaporation. And lastly, the MODIS Terrestrial Evapotranspiration (MOD16A2) which uses the Penman-Monteith equation as a basis to separately calculate the evaporative fluxes such as transpiration, soil evaporation, and interception. The outputs of the evaporation models differ quite a lot, especially during the transition period. This is among other things due to the input variable such as vegetation indices. There are several vegetation indices such as the Normalized Difference Vegetation Index (NDVI), the Normalized Difference Infrared Index (NDII) and the Leaf Area Index (LAI). The difference in the indexes is minimal and only small timing differences can be found. This means that the output differences are not influenced by the vegetation indices. MODIS follows the trends found by the vegetation indices best as it does not have the shortcomings that GLEAM and SEBS display. GLEAM overestimates the water stress because the model doesn’t account for plant water storage. While SEBS responds well until the start of July in which the model starts to oscillate. The oscillations could be due to the slash and burn culture which happens around this time which could impact SEBS substantially due to its dependency on temperature and radiation. Even if the MODIS output is the most similar to the vegetation output, it is limited by the fact that it is average values and daily variations might be lost. As this research is based on mostly satellite images supplemented by field observations, no statements can be made about it how accurate the models are. But based on this research, the MODIS model seems to be the preferred evaporation output.ZAMSECURCivil Engineerin
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