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Ha, S. (author), Tang, Y. (author), van Oene, M.M. (author), Janissen, R. (author), Dries, R.M. (author), Solano Hermosilla, B.P. (author), Adam, A.J.L. (author), Dekker, N.H. (author)
Optical trapping of (sub)micron-sized particles is broadly employed in nanoscience and engineering. The materials commonly employed for these particles, however, have physical properties that limit the transfer of linear or angular momentum (or both). This reduces the magnitude of forces and torques, and the spatiotemporal resolution,...
journal article 2019
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Al Nahas, K. (author), Cama, J. (author), Schaich, M. (author), Hammond, K. (author), Deshpande, S.R. (author), Dekker, C. (author), Ryadnov, M. G. (author), Keyser, UF (author)
The spread of bacterial resistance against conventional antibiotics generates a great need for the discovery of novel antimicrobials. Polypeptide antibiotics constitute a promising class of antimicrobial agents that favour attack on bacterial membranes. However, efficient measurement platforms for evaluating their mechanisms of action in a...
journal article 2019
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Deshpande, S.R. (author), Brandenburg, Frank (author), Lau, A.W.H.R. (author), Last, M.G.F. (author), Spoelstra, W.K. (author), Reese, L. (author), Wunnava, Sreekar (author), Dogterom, A.M. (author), Dekker, C. (author)
Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell biology, as it forms numerous membraneless organelles in cells. Coacervates play an indispensable role in regulating intracellular biochemistry, and their dysfunction is associated with several diseases. Understanding of the LLPS dynamics would...
journal article 2019
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Kabiri, Y. (author), Angelin, Alessandro (author), Ahmed, Ishtiaq (author), Mutlu, Hatice (author), Bauer, Jens (author), Niemeyer, Christof M. (author), Zandbergen, H.W. (author), Dekker, C. (author)
Staining compounds containing heavy elements (electron dyes) can facilitate the visualization of DNA and related biomolecules by using TEM. However, research into the synthesis and utilization of alternative electron dyes has been limited. Here, we report the synthesis of a novel DNA intercalator molecule, bis-acridine uranyl (BAU). NMR...
journal article 2019
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Fanalista, F. (author), Birnie, A.T.F. (author), Maan, R. (author), Burla, Federica (author), Charles usagé Charles-Carty, K.V. (author), Pawlik, G. (author), Deshpande, S.R. (author), Koenderink, Gijsje H. (author), Dogterom, A.M. (author), Dekker, C. (author)
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is...
journal article 2019
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Hol, F.J.H. (author), Whitesides, George M. (author), Dekker, C. (author)
Habitat spatial structure has a profound influence on bacterial life, yet there currently are no low-cost equipment-free laboratory techniques to reproduce the intricate structure of natural bacterial habitats. Here, we demonstrate the use of paper scaffolds to create landscapes spatially structured at the scales relevant to bacterial ecology...
journal article 2019
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Mouter, N. (author), Cabral, Manuel Ojeda (author), Dekker, T. (author), van Cranenburgh, Sander (author)
Environmental effects of transport projects have a weak position in Cost-Benefit Analysis (CBA) which might be rooted in the valuation approach adopted in the dominant style of CBA. This conventional valuation approach has been criticized for not valuing positive and negative impacts of transport projects in relation to each other and for not...
journal article 2019
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Dekker, R. (author), van der Meer, F.P. (author), Maljaars, J. (author), Sluijs, L.J. (author)
Structures are subjected to cyclic loads that can vary in direction and magnitude, causing constant amplitude mode I simulations to be too simplistic. This study presents a new approach for fatigue crack propagation in ductile materials that can capture mixed-mode loading and overloading. The extended finite element method is used to deal with...
journal article 2019
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Bracher, J.M. (author), Martinez-Rodriguez, Oscar A. (author), Dekker, W.J.C. (author), Verhoeven, M.D. (author), van Maris, A.J.A. (author), Pronk, J.T. (author)
Expression of a heterologous xylose isomerase, deletion of the GRE3 aldose-reductase gene and overexpression of genes encoding xylulokinase (XKS1) and non-oxidative pentose-phosphate-pathway enzymes (RKI1, RPE1, TAL1, TKL1) enables aerobic growth of Saccharomyces cerevisiae on d-xylose. However, literature reports differ on whether anaerobic...
journal article 2019
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Kabiri, Y. (author), Ravelli, Raimond B.G. (author), Lehnert, Tibor (author), Qi, Haoyuan (author), Katan, A.J. (author), Roest, Natascha (author), Kaiser, Ute (author), Dekker, C. (author), Peters, Peter J. (author), Zandbergen, H.W. (author)
Over the last few years, tremendous progress has been made in visualizing biologically important macromolecules using transmission electron microscopy (TEM) and understanding their structure-function relation. Yet, despite the importance of DNA in all forms of life, TEM visualization of individual DNA molecules in its native unlabeled form...
journal article 2019
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Zhao, Shidi (author), Restrepo Perez, L. (author), Soskine, Misha (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author), Aksimentiev, A. (author)
Ion channels form the basis of information processing in living cells by facilitating the exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires the development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations....
journal article 2019
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Lee, Kuo Ming (author), Gong, Yu Nong (author), Hsieh, Tzu Hsuan (author), Woodman, Andrew (author), Dekker, N.H. (author), Cameron, Craig E. (author), Shih, Shin Ru (author)
Enterovirus A71 (EV-A71) is an important nonpolio enterovirus that causes severe neurological complications. In 1998, Taiwan experienced an EV-A71 outbreak that caused 78 deaths. Since then, periodic epidemics of EV-A71 associated with newly emerging strains have occurred. Several of these strains are known to be recombinant; however, how...
journal article 2018
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van Oene, M.M. (author), Ha, S. (author), Jager, T. (author), Lee, M. (author), Pedaci, F. (author), Lipfert, J. (author), Dekker, N.H. (author)
Single-molecule manipulation techniques have provided unprecedented insights into the structure, function, interactions, and mechanical properties of biological macromolecules. Recently, the single-molecule toolbox has been expanded by techniques that enable measurements of rotation and torque, such as the optical torque wrench (OTW) and...
journal article 2018
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Ketterer, Philip (author), Ananth, A.N. (author), Laman Trip, J.D.S. (author), Mishra, Ankur (author), Bertosin, Eva (author), Ganji, M. (author), van der Torre, J. (author), Onck, Patrick (author), Dietz, Hendrik (author), Dekker, C. (author)
The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize artificial NPC mimics that allows controlling...
journal article 2018
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Joshi, S. (author), Savov, A.M. (author), Shafqat, Salman (author), Dekker, R. (author)
The authors found that oxygen plasma etching of polyimide (PI) with aluminum (Al) as a hard-etch mask results in lightly textured arbitrary shaped “fur-like” residues. Upon investigation, the presence of Al was detected in these residues. Ruling out several causes of metal contamination that were already reported in literature, a new theory for...
journal article 2018
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Savov, A.M. (author), Joshi, S. (author), Shafqat, Salman (author), Hoefnagels, Johan P.M. (author), Louwerse, M.C. (author), Stoute, R. (author), Dekker, R. (author)
A device for studying the mechanical and electrical behavior of free-standing micro-fabricated metal structures, subjected to a very large deformation, is presented in this paper. The free-standing structures are intended to serve as interconnects in high-density, highly stretchable electronic circuits. For an easy, damage-free handling and...
journal article 2018
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van Driel, B.A. (author), van den Berg, K. J. (author), Smout, M. (author), Dekker, N (author), Kooyman, P.J. (author), Dik, J. (author)
This study reports on the effect of artists’ paint formulation on degradation rates of TiO2-based oil paints. Titanium white oil paint exists in a multitude of different recipes, and the effect of the formulation on photocatalytic binder
degradation kinetics is unknown. These formulations contain, among others, one or both titanium dioxide...
journal article 2018
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Wiktor, J.M. (author), Sherratt, David J. (author), Dekker, C. (author)
The formation of 3 single-stranded DNA overhangs is a first and essential step during homology-directed repair of double-stranded breaks (DSB) of DNA, a task that in Escherichia coli is performed by RecBCD. While this protein complex has been well characterized through in vitro single-molecule studies, it has remained elusive how end...
journal article 2018
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Quiros Solano, W.F. (author), Gaio, N. (author), Stassen, O.M.J.A. (author), Arik, Y.B. (author), Silvestri, C. (author), Van Engeland, N.C.A. (author), van der Meer, A.D. (author), Passier, R. (author), Sahlgren, C.M. (author), Bouten, C.V.C. (author), van den Berg, A. (author), Dekker, R. (author), Sarro, P.M. (author)
We present a novel and highly reproducible process to fabricate transferable porous PDMS membranes for PDMS-based Organs-on-Chips (OOCs) using microelectromechanical systems (MEMS) fabrication technologies. Porous PDMS membranes with pore sizes down to 2.0 μm in diameter and a wide porosity range (2–65%) can be fabricated. To overcome issues...
journal article 2018
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Deshpande, S.R. (author), Spoelstra, W.K. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Liposomes, self-assembled vesicles with a lipid-bilayer boundary similar to cell membranes, are extensively used in both fundamental and applied sciences. Manipulation of their physical properties, such as growth and division, may significantly expand their use as model systems in cellular and synthetic biology. Several approaches have been...
journal article 2018
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