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Ganji, M. (author), Kim, S.H. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
DNA supercoiling crucially affects cellular processes such as DNA replication, gene expression, and chromatin organization. However, mechanistic understanding of DNA supercoiling and the related DNA-processing enzymes has remained limited, mainly due to the lack of convenient experimental tools to probe these phenomena. Here, we report a...
journal article 2016
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Wu, F. (author), Halatek, Jacob (author), Reiter, Matthias (author), Kingma, Enzo (author), Frey, Erwin (author), Dekker, C. (author)
Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during...
journal article 2016
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Wiktor, J.M. (author), Lesterlin, Christian (author), Sherratt, David J. (author), Dekker, C. (author)
Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein,...
journal article 2016
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Vtyurina, N. (author), Dulin, D. (author), Docter, M.W. (author), Meyer, A.S. (author), Dekker, N.H. (author), Abbondanzieri, E. (author)
In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively...
journal article 2016
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Dekker, N.H. (author), Ha, S. (author), Janissen, R. (author), Ussembayev, Y. (author), van Oene, M.M. (author), Solano Hermosilla, B.P. (author)
Titanium dioxide (TiO2) is a key component of diverse optical and electronic applications that exploit its exceptional material properties. In particular, the use of TiO2 in its single-crystalline phase can offer substantial advantages over its amorphous and polycrystalline phases for existing and yet-to-be-developed applications. However, the...
journal article 2016
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Eeftens, J.M. (author), Katan, A.J. (author), Kschonsak, Marc (author), Hassler, Markus (author), de Wilde, L. (author), Dief, Essam M. (author), Haering, Christian H. (author), Dekker, C. (author)
Structural maintenance of chromosomes (SMC) protein complexes, including cohesin and condensin, play key roles in the regulation of higher-order chromosome organization. Even though SMC proteins are thought to mechanistically determine the function of the complexes, their native conformations and dynamics have remained unclear. Here, we probe...
journal article 2016
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Hol, F.J.H. (author), Rotem, Or (author), Jurkevitch, Edouard (author), Dekker, C. (author), Koster, D. (author)
Soil is a microenvironment with a fragmented (patchy) spatial structure in which many bacterial species interact. Here, we explore the interaction between the predatory bacterium Bdellovibrio bacteriovorus and its prey Escherichia coli in microfabricated landscapes. We ask how fragmentation influences the prey dynamics at the microscale and...
journal article 2016
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Kim, S.H. (author), Vlijm, R. (author), van der Torre, J. (author), Dalal, Y. (author), Dekker, C. (author)
Centromere-specific nucleosomes are a central feature of the kinetochore complex during mitosis, in which microtubules exert pulling and pushing forces upon the centromere. CENP-A nucleosomes have been assumed to be structurally unique, thereby providing resilience under tension relative to their H3 canonical counterparts. Here, we directly test...
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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Hol, F.J.H. (author), Hubert, A.W.R. (author), Dekker, C. (author), Keymer Vergara, J.E. (author)
During antibiotic treatment, antibiotic concentration gradients develop. Little is know regarding the effects of antibiotic gradients on populations of nonresistant bacteria. Using a microfluidic device, we show that high-density motile Escherichia coli populations composed of nonresistant bacteria can, unexpectedly, colonize environments...
journal article 2016
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Moolman, M.C. (author), Tiruvadi Krishnan, S. (author), Kerssemakers, J.W.J. (author), de Leeuw, R. (author), Lorent, V.J.F. (author), Sherratt, David J. (author), Dekker, N.H. (author)
Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood....
journal article 2016
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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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Gaio, N. (author), Silvestri, C. (author), van Meer, B.J. (author), Vollebregt, S. (author), Mummery, CL (author), Dekker, R. (author)
Microelectrode arrays (MEAs) are widely used in biological application to locally stimulate and record the electrical activity of living cells. Here, a novel fabrication process for a carbon nanotube (CNT)-based MEA integrated on the backside of a free standing stretchable membrane is reported. The new<br/>process flow overcomes the manually...
journal article 2016
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Joshi, S. (author), Savov, A.M. (author), Dekker, R. (author)
This paper focuses on the implementation of a new technique for the fabrication of stretchable electronic patches that can be used for medical applications. The technique is based on the Electronics on Plastics by Laser Release (EPlaR) technology which enables a one-step release of a stack of flexible/stretchable layers incorporating the active...
journal article 2016
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Dekker, S.H. (author), Wurzel, G. (author), Alderliesten, R.C. (author)
Fatigue life is a random variable. The reliability of a conservative fatigue life prediction for a component in the helicopter dynamic system thus needs to be substantiated. A standard analytical substantiation method uses averaged manoeuvre loads instead of seeing manoeuvre loads as a random variable whose distribution is estimated with limited...
journal article 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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Stoute, R. (author), Louwerse, M.C. (author), Henneken, VA (author), Dekker, R. (author)
Minimally invasive surgery of the most lethal disease worldwide, coronary artery disease, benefits from better diagnostic tools during the treatment. With this in mind, a novel concept is introduced for intravascular ultrasound on a 360 μm diameter guidewire. The complex manufacture of this medical instrument, and other devices that require...
journal article 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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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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