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Waafi, Affan K. (author), Gaio, N. (author), Quiros Solano, W.F. (author), Dijkstra, Paul (author), Sarro, P.M. (author), Dekker, R. (author)
We present the first Organ-on-Chip equipped with a low-impedance Poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) MicroElectrode Array (MEA). The novel device allows simultaneous mechanical stimulation with a stretchable PDMS membrane and electrical monitoring via the PEDOT:PSS MEA of multiple in vitro cell cultures. The...
journal article 2020
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Last, M.G.F. (author), Deshpande, S.R. (author), Dekker, C. (author)
Membraneless organelles formed by liquid-liquid phase separation are dynamic structures that are employed by cells to spatiotemporally regulate their interior. Indeed, complex coacervation-based phase separation is involved in a multitude of biological tasks ranging from photosynthesis to cell division to chromatin organization, and more....
journal article 2020
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Smith, Kathleen Beth (author), Wehrli, Monika (author), Japaridze, A. (author), Assenza, Salvatore (author), Dekker, C. (author), Mezzenga, Raffaele (author)
The fine interplay between the simultaneous stretching and confinement of amyloid fibrils is probed by combining a microcapillary setup with atomic force microscopy. Single-molecule statistics reveal how the stretching of fibrils changed from force to confinement dominated at different length scales. System order, however, is solely ruled by...
journal article 2020
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Japaridze, A. (author), Gogou, Christos (author), Kerssemakers, J.W.J. (author), Nguyen, Huyen My (author), Dekker, C. (author)
The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move...
journal article 2020
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Caneva, S. (author), Hermans, Matthijs (author), Lee, M. (author), García-Fuente, Amador (author), Watanabe, Kenji (author), Taniguchi, Takashi (author), Dekker, C. (author), Ferrer, Jaime (author), van der Zant, H.S.J. (author), Gehring, P. (author)
Graphene quantum dots (QDs) are intensively studied as platforms for the next generation of quantum electronic devices. Fine tuning of the transport properties in monolayer graphene QDs, in particular with respect to the independent modulation of the tunnel barrier transparencies, remains challenging and is typically addressed using...
journal article 2020
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Kaczmarczyk, A.P. (author), Meng, He (author), Ordu, O. (author), Noort, John van (author), Dekker, N.H. (author)
Torsional stress generated during DNA replication and transcription has been suggested to facilitate nucleosome unwrapping and thereby the progression of polymerases. However, the propagation of twist in condensed chromatin remains yet unresolved. Here, we measure how force and torque impact chromatin fibers with a nucleosome repeat length of...
journal article 2020
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Kim, E. (author), Kerssemakers, J.W.J. (author), Shaltiel, Indra A. (author), Haering, Christian H. (author), Dekker, C. (author)
Condensin, a key component of the structure maintenance of chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA<sup>1</sup>. It remains unclear, however, how condensin complexes work together to collectively package DNA into chromosomes. Here we use time-lapse single-molecule visualization to...
journal article 2020
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Størkersen, Kristine (author), Thorvaldsen, Trine (author), Kongsvik, Trond (author), Dekker, S.W.A. (author)
Over the past decades, government safety management regulation has been driven by deregulation, simplification and organization-level regimes of inspection. So-called functional rule-making requires organizations to implement safety management systems appropriate for their operations. The paradox that seems to have arisen is that...
journal article 2020
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van der Meij, Leander (author), Demetriou, A.M. (author), Tulin, Marina (author), Méndez, Ileana (author), Dekker, Peter (author), Pronk, Tila (author)
There is evidence that testosterone and cortisol levels are related to the attraction of a romantic partner; testosterone levels relate to a wide range of sexual behaviors and cortisol is a crucial component in the response to stress. To investigate this, we conducted a speed-dating study among heterosexual singles. We measured salivary...
journal article 2019
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Dekker, W.J.C. (author), Wiersma, S.J. (author), Bouwknegt, J. (author), Mooiman, C. (author), Pronk, J.T. (author)
In Saccharomyces cerevisiae, acyl-coenzyme A desaturation by Ole1 requires molecular oxygen. Tween 80, a poly-ethoxylated sorbitan-oleate ester, is therefore routinely included in anaerobic growth media as a source of unsaturated fatty acids (UFAs). During optimization of protocols for anaerobic bioreactor cultivation of this yeast, we...
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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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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Wu, Fabai (author), Japaridze, A. (author), Zheng, X.Z. (author), Wiktor, J.M. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)
Although the physical properties of chromosomes, including their morphology, mechanics, and dynamics are crucial for their biological function, many basic questions remain unresolved. Here we directly image the circular chromosome in live E. coli with a broadened cell shape. We find that it exhibits a torus topology with, on average, a lower...
journal article 2019
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Restrepo Perez, L. (author), Huang, Gang (author), Bohländer, Peggy R. (author), Worp, N.M. (author), Eelkema, R. (author), Maglia, Giovanni (author), Joo, C. (author), Dekker, C. (author)
While DNA sequencing is now amply available, fast, and inexpensive, protein sequencing remains a tremendous challenge. Nanopores may allow for developing a protein sequencer with single-molecule capabilities. As identification of 20 different amino acids currently presents an unsurmountable challenge, fingerprinting schemes are pursued, in...
journal article 2019
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Quiros Solano, W.F. (author), Gaio, N. (author), Silvestri, C. (author), Pandraud, G. (author), Dekker, R. (author), Sarro, P.M. (author)
Organ-on-chip (OOC) is becoming the alternative tool to conventional in vitro screening. Heart-on-chip devices including microstructures for mechanical and electrical stimulation have been demonstrated to be advantageous to study structural organization and maturation of heart cells. This paper presents the development of metal and polymeric...
journal article 2019
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Schaich, Michael (author), Cama, Jehangir (author), Al Nahas, Kareem (author), Sobota, Diana (author), Sleath, Hannah (author), Jahnke, Kevin (author), Deshpande, S.R. (author), Dekker, C. (author), Keyser, Ulrich F. (author)
The low membrane permeability of candidate drug molecules is a major challenge in drug development, and insufficient permeability is one reason for the failure of antibiotic treatment against bacteria. Quantifying drug transport across specific pathways in living systems is challenging because one typically lacks knowledge of the exact...
journal article 2019
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Mountain, Christopher (author), Kluba, M.M. (author), Bergers, L.I.J.C. (author), Snijder, Jaap (author), Dekker, R. (author)
Accurate alignment between the cavities in cavity-SOI (c-SOI) wafers and lithography on the wafer surface is essential to advanced MEMS production. Existing alignment methods are well defined, but often require specialized equipment or costly software packages available only in professional manufacturing environments. It would be beneficial...
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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Cudejko, Tomasz (author), van der Esch, Martin (author), van den Noort, Josien C. (author), Rijnhart, Judith J.M. (author), van der Leeden, Marike (author), Roorda, Leo D. (author), Lems, Willem (author), Waddington, Gordon (author), Harlaar, J. (author), Dekker, Joost (author)
Objective: To evaluate whether improvement of proprioception, pain, or dynamic knee instability mediates the effect of wearing a soft knee brace on activity limitations in patients with knee osteoarthritis (OA). Methods: We conducted an analysis of data for 44 patients with knee OA who were enrolled in a laboratory-based trial evaluating the...
journal article 2019
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Verschueren, Daniel (author), Shi, X. (author), Dekker, C. (author)
Single-molecule sensing technologies aim to detect and characterize single biomolecules, but generally need labeling while the measurement times and throughput are severely restricted by a lack of positional control over the molecule. Here, a plasmonic nanopore biosensor is reported where single molecules can be electrophoretically delivered...
journal article 2019
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