Searched for: subject%3A%22DNA%22
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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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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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Borg, 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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Yang, X. (author), Guo, Fucheng (author), Liu, Tao (author), He, Qiang (author), Vymazal, Jan (author), Chen, Yi (author)
Ammonia-oxidizing microorganisms (AOMs, archaea (AOA) and bacteria (AOB)) are primarily responsible for the ammoxidation in constructed wetlands (CWs). However, little is known about evaluating the response of AOA and AOB to engineered nanomaterials (ENMs) and quantifying the shift of their contribution to ammoxidation. Herein, we operated a...
journal article 2023
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Tang, Yuchen (author), van Rhijn, Fay (author), Abdelrady, Ahmed (author), Foppen, J.W.A. (author), Bogaard, T.A. (author)
Recently, superparamagnetic silica encapsulated DNA microparticles (SiDNAFe) were designed and in various experiments used as a hydrological tracer. We investigated the effect of bed characteristics on the transport behaviour and especially the mass loss of SiDNAFe in open channel injection experiments. Hereto, a series of laboratory...
journal article 2023
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Abil, Z. (author), Restrepo Sierra, A.M. (author), Danelon, C.J.A. (author)
In cell-free gene expression, low input DNA concentration severely limits the phenotypic output, which may impair in vitro protein evolution efforts. We address this challenge by developing CADGE, a strategy that is based on clonal isothermal amplification of a linear gene-encoding dsDNA template by the minimal Φ29 replication machinery and...
journal article 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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Nick Maleki, A. (author), Huis In 't Veld, Pim J. (author), Akhmanova, Anna (author), Dogterom, A.M. (author), Volkov, V. (author)
Microtubules are dynamic cytoskeletal filaments that can generate forces when polymerizing and depolymerizing. Proteins that follow growing or shortening microtubule ends and couple forces to cargo movement are important for a wide range of cellular processes. Quantifying these forces and the composition of protein complexes at dynamic...
journal article 2023
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Tang, Yuchen (author), Zhang, Fengbo (author), Bogaard, T.A. (author), Chassagne, C. (author), Ali, Zeeshan (author), Bandyopadhyay, Sulalit (author), Foppen, J.W.A. (author)
Particle tracers are sometimes used to track sources and sinks of riverine particulate and contaminant transport. A potentially new particle tracer is ~200 nm sized superparamagnetic silica encapsulated DNA (SiDNAFe). The main objective of this research was to understand and quantify the settling and aggregation behaviour of SiDNAFe in river...
journal article 2023
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Fernandes, Maria (author), Decouchant, Jérémie (author), Couto, Francisco M. (author)
DNA computing is an emerging field that aims at enabling more efficient data storage and processing. One principle of DNA computing is to encode some information (e.g., image, video, programming scripts) into a digital DNA-like sequence and then synthesize the corresponding DNA molecule. Synthesizing this molecule using digital or real human...
book chapter 2023
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Sørli, Jorid B. (author), Jensen, Alexander C.Ø. (author), Mortensen, Alicja (author), Szarek, Józef (author), Gutierrez, Claudia A.T. (author), Givelet, Lucas (author), Loeschner, Katrin (author), Loizides, Charis (author), Biskos, G. (author)
Molybdenum disulphide (MoS<sub>2</sub>) is a constituent of many products. To protect humans, it is important to know at what air concentrations it becomes toxic. For this, we tested MoS<sub>2</sub> particles by nose-only inhalation in mice. Exposures were set to 13, 50 and 150 mg MoS<sub>2</sub>/m<sup>3</sup> (=8, 30 and 90 mg Mo/m<sup>3<...
journal article 2023
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Sakata, Dousatsu (author), Hirayama, Ryoichi (author), Shin, Wook Geun (author), Belli, Mauro (author), Tabocchini, Maria A. (author), Stewart, Robert D. (author), Brown, J.M.C. (author), Kyriakou, G.I. (author), Tran, Hoang N. (author)
Purpose: Track structure Monte Carlo (MC) codes have achieved successful outcomes in the quantitative investigation of radiation-induced initial DNA damage. The aim of the present study is to extend a Geant4-DNA radiobiological application by incorporating a feature allowing for the prediction of DNA rejoining kinetics and corresponding cell...
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
Searched for: subject%3A%22DNA%22
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