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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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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), 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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Dekker, S.H. (author)
A mechanical component can break due to repeated load cycling, even if these loads remain well below the component’s regular static strength. In a simplified fashion, a component’s fatigue life depends on the loads that it has to endure during its service life, as well as its fatigue strength to resist the formation of cracks. Since both of...
doctoral thesis 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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Kim, S.H. (author), Ganji, M. (author), Kim, E. (author), van der Torre, J. (author), Abbondanzieri, E. (author), Dekker, C. (author)
The three-dimensional organization of DNA is increasingly understood to play a decisive role in vital cellular processes. Many studies focus on the role of DNA-packaging proteins, crowding, and confinement in arranging chromatin, but structural information might also be directly encoded in bare DNA itself. Here, we visualize plectonemes ...
journal article 2018
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Yang, W.W.W. (author), Restrepo Perez, L. (author), Bengtson, M.L. (author), Heerema, S.J. (author), Birnie, A.T.F. (author), van der Torre, J. (author), Dekker, C. (author)
Solid-state nanopores have emerged as promising platforms for biosensing including diagnostics for disease detection. Here we show nanopore experiments that detect CRISPR-dCas9, a sequence-specific RNA-guided protein system that specifically binds to a target DNA sequence. While CRISPR-Cas9 is acclaimed for its gene editing potential, the...
journal article 2018
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Ordu, O. (author), Kremser, Leopold (author), Lusser, Alexandra (author), Dekker, N.H. (author)
Nucleosomes consisting of a short piece of deoxyribonucleic acid (DNA) wrapped around an octamer of histone proteins form the fundamental unit of chromatin in eukaryotes. Their role in DNA compaction comes with regulatory functions that impact essential genomic processes such as replication, transcription, and repair. The assembly of...
journal article 2018
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Spoelstra, W.K. (author), Deshpande, S.R. (author), Dekker, C. (author)
Recently, the bottom-up assembly of a synthetic cell has emerged as a daring novel approach that can be expected to have major impact in generating fundamental insight in the organization and function of actual biological cells, as well as in stimulating a broad range of applications from drug delivery systems to chemical nanofactories. A...
review 2018
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Restrepo Perez, L. (author), Joo, C. (author), Dekker, C. (author)
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example,...
review 2018
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Fanalista, F. (author), Deshpande, S.R. (author), Lau, A.W.H.R. (author), Pawlik, G. (author), Dekker, C. (author)
Recently, both the cellular and synthetic biology communities have expressed a strong interest in coacervates, membrane‐less liquid droplets composed of densely packed multivalent molecules that form as a result of spontaneous phase separation. Here, it is studied how FtsZ, a protein that plays a key role in the bacterial division process,...
journal article 2018
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Jansen, A.J. (author), Dekker, M.C. (author), van der Steen, Diederik (author)
Providing athletes with real-time feedback on their performance is becoming common in many sports, also in speed skating. This research-by-design project aims at finding a tool that allows the speed skater to get real-time feedback on his performance. Speed skaters often mention a so-called “good feeling” when skating behind a better skater. It...
conference paper 2018
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Caspi, Y. (author), Dekker, C. (author)
Cell division in most prokaryotes is mediated by the well-studied fts genes, with FtsZ as the principal player. In many archaeal species, however, division is orchestrated differently. The Crenarchaeota phylum of archaea features the action of the three proteins, CdvABC. This Cdv system is a unique and less-well-studied division mechanism that...
journal article 2018
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Verschueren, D.V. (author), Pud, S. (author), Shi, X. (author), de Angelis, L. (author), Kuipers, L. (author), Dekker, C. (author)
Solid-state nanopores are single-molecule sensors that hold great potential for rapid protein and nucleic-acid analysis. Despite their many opportunities, the conventional ionic current detection scheme that is at the heart of the sensor suffers inherent limitations. This scheme intrinsically couples signal strength to the driving voltage,...
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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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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Verschueren, D.V. (author), Yang, W.W.W. (author), Dekker, C. (author)
We report a simple and scalable technique for the fabrication of nanopore arrays on freestanding SiN and graphene membranes based on electron-beam lithography and reactive ion etching. By controlling the dose of the single-shot electron-beam exposure, circular nanopores of any size down to 16 nm in diameter can be fabricated in both materials...
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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Deshpande, S.R. (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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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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