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Ordu, O. (author), Lusser, A (author), Dekker, N.H. (author)
Eukaryotic DNA is tightly packed into a hierarchically ordered structure called chromatin in order to fit into the micron-scaled nucleus. The basic unit of chromatin is the nucleosome, which consists of a short piece of DNA wrapped around a core of eight histone proteins. In addition to their role in packaging DNA, nucleosomes impact the...
journal article 2016
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Wu, F. (author), Dekker, C. (author)
Nanofabricated structures and microfluidic technologies are increasingly being used to study bacteria because of their precise spatial and temporal control. They have facilitated studying many long-standing questions regarding growth, chemotaxis and cell-fate switching, and opened up new areas such as probing the effect of boundary geometries...
review 2016
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Heerema, S.J. (author), Dekker, C. (author)
Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and...
journal article 2016
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Deshpande, S.R. (author), Caspi, Y. (author), Meijering, A.E.C. (author), Dekker, C. (author)
Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5–20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a...
journal article 2016
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Dekker, G. (author), Nootenboom, T. (author), Locher, L. (author), Spekkers, M.H. (author)
In het Impactproject ‘Samen met verzekeraars naar een regenbestendige stad’ hebben we de werelden van een verzekeraar, onderzoeker en gemeente/waterbeheerder bij elkaar gebracht. Amsterdam Rainproof, Waternet, Achmea en TU Delft zijn de samenwerking aangegaan om de impact van extreme regenval op bewoners in Amsterdam te analyseren en te...
report 2016
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Vlijm, R. (author), Torre, J. (author), Dekker, C. (author)
The metabolism of DNA in cells relies on the balance between hybridized double-stranded DNA (dsDNA) and local de-hybridized regions of ssDNA that provide access to binding proteins. Traditional melting experiments, in which short pieces of dsDNA are heated up until the point of melting into ssDNA, have determined that AT-rich sequences have a...
journal article 2015
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Vlijm, R. (author), Lee, M. (author), Ordu, O. (author), Boltengagen, A. (author), Lusser, A. (author), Dekker, N.H. (author), Dekker, C. (author)
Eukaryotic nucleosomes consists of an (H3-H4)2 tetramer and two H2A-H2B dimers, around which 147 bp of DNA are wrapped in 1.7 left-handed helical turns. During chromatin assembly, the (H3-H4)2 tetramer binds first, forming a tetrasome that likely constitutes an important intermediate during ongoing transcription. We recently showed that (H3-H4)2...
journal article 2015
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Vervoorn, R.R.E. (author), Dekker, H.R.E. (author)
Rijkswaterstaat has recently stated that the use of GeoRM is obligatory for projects with major geotechnical risks. Underground construction of freeway's in high-profile areas, such as the business district Zuidas in Amsterdam or railway links in densely populated areas, always introduce major geotechnical risks. It is not uncommon for these...
conference paper 2015
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Dekker, R. (author), Henneken, V.A. (author), Louwerse, M.C. (author), Raganato, M.F. (author)
The present invention relates to an ultrasound transducer assembly (10), in particular for intravascular ultrasound systems. The ultrasound transducer assembly comprises at least one silicon substrate element (30) including an ultrasound transducer element (14) for emitting and receiving ultrasound waves and including electrical connectors for...
patent 2015
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Plesa, C. (author), Van Loo, N. (author), Dekker, C. (author)
Nanopore experiments have traditionally been carried out with chloride-based solutions. Here we introduce silver/silver-glutamate-based electrochemistry as an alternative, and study the viscosity, conductivity, and nanopore translocation characteristics of potassium-, sodium-, and lithium-glutamate solutions. We show that it has a linear...
journal article 2015
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Krishnan, S.T. (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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Hol, F.J.H. (author), Galajda, P. (author), Woolthuis, R.G. (author), Dekker, C. (author), Keymer, J.E. (author)
Background The spatial structure of a habitat can have a strong impact on community dynamics. Different experimental approaches exist to explore the effect of spatial structure on bacterial communities. To investigate the effect of ‘space’, a single implementation of spatial structure is often contrasted to bacterial community dynamics in well...
journal article 2015
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Van Oene, M.M. (author), Dickinson, L.E. (author), Pedaci, F. (author), Köber, M. (author), Dulin, D. (author), Lipfert, J. (author), Dekker, N.H. (author)
Superparamagnetic beads are widely used in biochemistry and single-molecule biophysics, but the nature of the anisotropy that enables the application of torques remains controversial. To quantitatively investigate the torques experienced by superparamagnetic particles, we use a biological motor to rotate beads in a magnetic field and demonstrate...
journal article 2015
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Klein, S. (author), Vast, E. (author), Van Soest, J. (author), Dekker, A. (author), Koek, M. (author), Niessen, W.J. (author)
1st Clinical Research Informatics (CRI) Solutions Day Duesseldorf, Germany, 26-27 May 2014
journal article 2015
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Stoute, R. (author), Louwerse, M.C. (author), Van Rens, J. (author), Henneken, V.A. (author), Dekker, R. (author)
We propose a novel concept for a high-speed optical data link in Ø 360 µm cardiovascular interventional imaging guidewires. The concept is based on the recently introduced Flex-to-Rigid (F2R) technology platform. This technology allows for smaller intravascular imaging devices with a more compact form-factor. We extended the existing F2R...
conference paper 2015
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Dekker, M.C. (author), Van Lochem, A.J. (author), Molenbroek, J.F.M. (author)
A healthy work-to-rest ratio during computer work can be an important part of successful preventive workrelated upper limb disorders (WRULD) intervention. Existing break software applications designed to realise such a work-to-rest ratio often possess product features that limit their functionality. Most applications focus on physical relaxation...
journal article 2015
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Dulin, D. (author), Vilfan, I.D. (author), Berghuis, B.A. (author), Hage, S. (author), Bamford, D.H. (author), Poranen, M.M. (author), Depken, S.M. (author), Dekker, N.H. (author)
RNA viruses have specific mutation rates that balance the conflicting needs of an evolutionary response to host antiviral defenses and avoidance of the error catastrophe. While most mutations are known to originate in replication errors, difficulties of capturing the underlying dynamics have left the mechanochemical basis of viral mutagenesis...
journal article 2015
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De Been, I. (author), Thoolen, F. (author), Cox, H. (author), Dekker, K. (author), Van Erpers Roijaards, F. (author), Mollerus, R. (author), Schols, I. (author)
report 2015
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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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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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