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Bastiaanssen, C.K.J.M.L. (author)Interactions are essential to life. At the cellular level, the most fundamental processes rely on interactions between DNA, RNA, and proteins. Given that the structure and function of these molecules are determined by their sequence, it is ultimately the sequence that dictates the strength and specificity of these interactions. Thus, to improve...doctoral thesis 2024
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Barth, R. (author)Genetic information encoded in the DNA sequences is maintained, replicated, and transcribed across the tree of life. Organisms evolved multiple hierarchical layers of chromosome organization which ensure that DNA can be contained but also processed within individual cells. This thesis focuses on SMC (Structural Maintenance of Chromosomes)...doctoral thesis 2024
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- Ramirez Montero, D.F. (author) doctoral thesis 2024
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Quiroga Fonseca, Valentina (author)Multivalent interactions are crucial mechanisms employed by cells to respond to their environment, often leading to superselectivity phenomena. Extensive experimental and theoretical efforts have been made to understand the variables controlling superselectivity, but challenges persist in achieving precise control over receptor and ligand...master thesis 2024
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Restrepo Sierra, A.M. (author)Life, the most complex and admirable machine that one could think of has evolved over billions of years to display a beautiful variety of mechanisms that keep cells adapting, self-maintaining, reproducing, and evolving. If we think about it, what is this magic? What are the mechanisms behind life’s origins and wonderful coordination? Attracted...doctoral thesis 2024
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Tišma, M. (author)This thesis explores the mechanisms that underlie chromosome organization in bacteria. Bacteria are considered amongst the simplest living organisms on our planet. They lack the cellular organization found in other domains of life (Archaea or Eukaryotics) and often have simpler life cycles. Over the past decade, we gained increasing knowledge...doctoral thesis 2024
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Dercksen, J.A. (author), Stancanelli, L.M. (author), Trimbos, Krijn B. (author), Blom, A. (author)River restoration is an established method for the rehabilitation of river ecosystems in order to combat the current declines of freshwater biodiversity (Wohl et al., 2005; WWF, 2022). The urgency of restoration is recognized internationally, as the IUCN has proclaimed 2021-2030 to be the ‘Decade on Ecosystem Restoration’ (Cooke et al., 2022)....abstract 2024
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Liu, Z. (author), van Veen, E.N.W. (author), Sanchez González, H. (author), Solano Hermosilla, B.P. (author), Palmero Moya, F.J.P.M. (author), Mc Cluskey, K.A. (author), Ramirez Montero, D.F. (author), van Laar, T. (author), Dekker, N.H. (author)Integrated single-molecule force-fluorescence spectroscopy setups allow for simultaneous fluorescence imaging and mechanical force manipulation and measurements on individual molecules, providing comprehensive dynamic and spatiotemporal information. Dual-beam optical tweezers (OT) combined with a confocal scanning microscope form a force...journal article 2024
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Abdelrady, Ahmed (author), Tang, Yuchen (author), Bogaard, T.A. (author), Foppen, J.W.A. (author)Sand filtration systems (SF) are a well-established approach in ensuring the availability of clean water. Understanding the transport properties of colloidal particles within SF systems is of paramount importance for optimizing their performance. This study investigated the potential utilization of silica-encapsulated DNA particles, equipped...journal article 2024
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Tubiana, Luca (author), Alexander, Gareth P. (author), Barbensi, Agnese (author), Buck, Dorothy (author), Cartwright, Julyan H.E. (author), Chwastyk, Mateusz (author), Cieplak, Marek (author), Coluzza, Ivan (author), Japaridze, A. (author)The last years have witnessed remarkable advances in our understanding of the emergence and consequences of topological constraints in biological and soft matter. Examples are abundant in relation to (bio)polymeric systems and range from the characterization of knots in single polymers and proteins to that of whole chromosomes and polymer melts....review 2024
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Putri, Ratna E. (author), Vrouwenvelder, J.S. (author), Farhat, Nadia (author)DNA extraction yield from drinking water distribution systems and premise plumbing is a key metric for any downstream analysis such as 16S amplicon or metagenomics sequencing. This research aimed to optimize DNA yield from low-biomass (chlorinated) reverse osmosis-produced tap water by evaluating the impact of different factors during the DNA...journal article 2024
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Kesapidou, Evi (author)Nanopores are narrow channels in cell membranes that control the passage of small molecules. In recent years, they have been repurposed for diverse applications, including single molecule sensing and drug delivery. Due to the small diameters of conventional protein-based, current research efforts are directed to designing nanopores from other...master thesis 2023
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Tang, Yuchen (author)Rivers are vital for maintaining freshwater ecosystems as they distribute nutrients as well as dilute and transport anthropogenic pollution. Tracers provide direct empirical data on complex waterflows and reveal transport processes of waterborne substances. Recent advances in material engineering and biomolecular technology have made it possible...doctoral thesis 2023
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Representations of DNA Sequence Context and Mutational Spectra for Prediction of Repair DeficienciesBorg, Jonathan (author)Double-strand break (DSB) repair is a critical cellular process which repairs breaks in both strands of the DNA double helix. Different repair mechanisms are tasked with repairing such breaks. Predicting deficiencies in repair mechanisms has been widely used for therapeutic purposes, such as targeting cancer cells that have specific DNA repair...master thesis 2023
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- Kruit, Vincent (author) master thesis 2023
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Miao, Michael (author)Due to recent developments in DNA sequencing technology, there is a growing abundance of available genomic data. To process this information for use in fields such as healthcare and forensics, raw sequencing data have to be processed using computationally intensive algorithms. Currently, one of the major bottlenecks in this processing pipeline...master thesis 2023
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Amini Hounejani, R. (author)The past decades have seen the rapid development of many aspects of synthetic biology. For example, attempts to build synthetic cells under controlled conditions in the laboratory have led to significant achievements. Following a bottom-up approach, scientists aim at building a self-reproducing synthetic cell with a minimum number of biological...doctoral thesis 2023
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Gil Jimenez, A. (author), van Dorp, Jeroen (author), Contreras-Sanz, Alberto (author), van der Vos, Kristan (author), Vis, Daniel J. (author), Braaf, Linde (author), Broeks, Annegien (author), Kerkhoven, Ron (author), van Kessel, Kim E.M. (author), Wessels, L.F.A. (author)Cisplatin-based neoadjuvant chemotherapy (NAC) followed by radical cystectomy is recommended for patients with muscle-invasive bladder cancer (MIBC). It has been shown that somatic deleterious mutations in ERCC2, gain-of-function mutations in ERBB2, and alterations in ATM, RB1, and FANCC are correlated with pathological response to NAC in...journal article 2023
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Foppen, J.W.A. (author)The use of artificial DNA (artDNA) in hydrological applications is becoming increasingly popular, either in dissolved form (dissolved artDNA) or encapsulated and protected by a layer (encDNA). DNA can be detected even at low concentrations and offers the ability to create numerous uniquely identifiable DNA labels, making it ideal for a wide...review 2023
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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...review 2023