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Vlijm, R. (author), Lee, M. (author), Lipfert, J. (author), Lusser, A. (author), Dekker, C. (author), Dekker, N.H. (author)DNA wrapping around histone octamers generates nucleosomes, the basic compaction unit of eukaryotic chromatin. Nucleosome stability is carefully tuned to maintain DNA accessibility in transcription, replication, and repair. Using freely orbiting magnetic tweezers, which measure the twist and length of single DNA molecules, we monitor the real...journal article 2015
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Tiruvadi Krishnan, S. (author), Moolman, M.C. (author), van Laar, T. (author), Meyer, A.S. (author), Dekker, N.H. (author)Background: Chromosome engineering encompasses a collection of homologous recombination-based techniques that are employed to modify the genome of a model organism in a controlled fashion. Such techniques are widely used in both fundamental and industrial research to introduce multiple insertions in the same Escherichia coli strain. To date,...journal article 2015
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Dulin, D. (author), Berghuis, B.A. (author), Depken, S.M. (author), Dekker, N.H. (author)Single-molecule experiments provide a unique means for real-time observation of the activity of individual biomolecular machines. Through such techniques, insights into the mechanics of for example, polymerases, helicases, and packaging motors have been gleaned. Here we describe the recent advances in single-molecule force spectroscopy...journal article 2015
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Berghuis, B.A. (author), Dulin, D. (author), Xu, Zhi Qiang (author), van Laar, T. (author), Cross, B. (author), Janissen, R. (author), Jergic, Slobodan (author), Dixon, Nicholas E. (author), Depken, S.M. (author), Dekker, N.H. (author)The bidirectional replication of a circular chromosome by many bacteria necessitates proper termination to avoid the head-on collision of the opposing replisomes. In Escherichia coli, replisome progression beyond the termination site is prevented by Tus proteins bound to asymmetric Ter sites. Structural evidence indicates that strand...journal article 2015
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Herfst, R. (author), Dekker, B. (author), Witvoet, G. (author), Crowcombe, W.E. (author), de Lange, D. (author), Sadeghian Marnani, H. (author)One of the major limitations in the speed of the atomic force microscope (AFM) is the bandwidth of the mechanical scanning stage, especially in the vertical (z) direction. According to the design principles of “light and stiff” and “static determinacy,” the bandwidth of the mechanical scanner is limited by the first eigenfrequency of the AFM...journal article 2015
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- Lipfert, J. (author), van Oene, M.M. (author), Lee, M. (author), Pedaci, F. (author), Dekker, N.H. (author) journal article 2015
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- Thoolen, F. (author), De Been, I. (author), Beijer, M. (author), Dekker, K. (author) report 2014
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), Van den Berg, A. (author), Tulinski, P. (author), Depken, M. (author), Reyes-Lamothe, R. (author), Sherratt, D.J. (author), Dekker, N.H. (author)The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli ?2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both ?2-clamp...journal article 2014
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Schneider, G.F. (author), Dekker, C. (author)The present invention is in the field of highly crystalline graphene and coating said graphene with a layer. Said graphene may have further structures, such as nanopores, nanogaps, and nanoribbons. The coated graphene can be used for biomolecular analysis and modification, such as DNA-sequencing, as a sensor, etc. The invention therefor also...patent 2014
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Burnham, D.R. (author), De Vlaminck, I. (author), Henighan, T. (author), Dekker, C. (author)Measurements in magnetic tweezers rely upon precise determination of the position of a magnetic microsphere. Fluctuations in the position due to Brownian motion allows calculation of the applied force, enabling deduction of the force-extension response function for a single DNA molecule that is attached to the microsphere. The standard approach...journal article 2014
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Ferrari, A.C. (author), Dekker, C. (author), Vandersypen, L.M.K. (author), Van Der Zant, H.S.J. (author)We present the science and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems, targeting an evolution in technology, that might lead to impacts and benefits reaching into most areas of society. This roadmap was developed within the framework of the European Graphene Flagship and outlines the main targets and...journal article 2014
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Hol, F.J.H. (author), Voges, M.J. (author), Dekker, C. (author), Keymer, J.E. (author)Background: Antagonistic interactions mediated by antibiotics are strong drivers of bacterial community dynamics which shape biodiversity. Colicin production by Escherichia coli is such an interaction that governs intraspecific competition and is involved in promoting biodiversity. It is unknown how environmental cues affect regulation of the...journal article 2014
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Janissen, R. (author), Berghuis, B.A. (author), Dulin, D. (author), Wink, M. (author), Van Laar, T. (author), Dekker, N.H. (author)Magnetic tweezers are a powerful single-molecule technique that allows real-time quantitative investigation of biomolecular processes under applied force. High pulling forces exceeding tens of picoNewtons may be required, e.g. to probe the force range of proteins that actively transcribe or package the genome. Frequently, however, the...journal article 2014
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Hertzberger, R. (author), Arents, J. (author), Dekker, H.L. (author), Pridmore, D. (author), Gysler, C. (author), Kleerebezem, M. (author), Teixeira de Mattosa, M.J. (author)Hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. In the presence of oxygen, the probiotic lactic acid bacterium Lactobacillus johnsonii NCC 533 excretes up to 1 mM H2O2, inducing growth stagnation and cell death. Disruption of genes commonly assumed to be involved in H2O2 production (e...journal article 2014
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Joo, C. (author), Dekker, C. (author), Van Ginkel, H.G.T.M. (author), Meyer, A.S. (author)The invention provides a device for determining the type of protein in a liquid, the device comprising (a) an immobilized ATP dependent protease based molecular transporter machine configured to guide a protein that is functionalized with labels through a detection area of a detector, (b) said detector, configured to detect a signal as function...patent 2014
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- Dekker, M. (author) master thesis 2014
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- Van Hal, J.D.M. (author), Van Sprundel, M. (author), Dekker, T.J. (author), Van der Heijden, H.M.H. (author) book chapter 2014
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Hol, F.J.H. (author), Galajda, P. (author), Nagy, K. (author), Woolthuis, R.G. (author), Dekker, C. (author), Keymer, J.E. (author)Cooperative organisms are ubiquitous in nature, despite their vulnerability to exploitation by cheaters. Although numerous theoretical studies suggest that spatial structure is critical for cooperation to persist, the spatial ecology of microbial cooperation remains largely unexplored experimentally. By tracking the community dynamics of...journal article 2013
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Van Riessen, B. (author), Negenborn, R.R. (author), Dekker, R. (author), Lodewijks, G. (author)An intermodal container transportation network is being developed between Rotterdam and several inland terminals in North West Europe: the EUROPEAN GATEWAY SERVICES network. This network is developed and operated by the sea terminals of EUROPE CONTAINER TERMINALS (ECT). To use this network cost-efficiently, centralised planning by the sea...journal article 2013
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Dekker, T. (author), Van Cranenburgh, S. (author), Chorus, C.G. (author)Choice probabilities and related outputs of discrete choice models form a critical input to many travel demand forecasting and transport project evaluation studies. The decision rule underlying a discrete choice model describes how individuals make their decisions and thereby co-determines the choice probabilities. Uncertainty from the side of...conference paper 2013