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Chakrabarty, Sanjiban (author), Quiros Solano, W.F. (author), Kuijten, Maayke M.P. (author), Haspels, Ben (author), Mallya, Sandeep (author), van de Stolpe, Anja (author), Odijk, Hanny (author), van Weerden, Wytske M. (author), Dekker, R. (author)Optimal treatment of cancer requires diagnostic methods to facilitate therapy choice and prevent ineffective treatments. Direct assessment of therapy response in viable tumor specimens could fill this diagnostic gap. Therefore, we designed a microfluidic platform for assessment of patient treatment response using tumor tissue slices under...journal article 2022
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Ryu, J.K. (author), Rah, S.H. (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Bonato, Andrea (author), Michieletto, Davide (author), Dekker, C. (author)The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion...journal article 2022
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Saccher, M. (author), Kawasaki, S. (author), Proietti Onori, Martina (author), van Woerden, Geeske M. (author), Giagka, Vasiliki (author), Dekker, R. (author)Background<br/>Microelectrode arrays (MEA) enable the measurement and stimulation of the electrical activity of cultured cells. The integration of other neuromodulation methods will significantly enhance the application range of MEAs to study their effects on neurons. A neuromodulation method that is recently gaining more attention is focused...journal article 2022
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Tišma, M. (author), Panoukidou, Maria (author), Antar, Hammam (author), Soh, Young Min (author), Barth, R. (author), Pradhan, B. (author), Barth, A. (author), van der Torre, J. (author), Dekker, C. (author)The ParABS system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzzling how this large-distance spreading can occur along DNA loaded with hundreds of proteins. Using in...journal article 2022
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Würthner, Laeschkir (author), Brauns, Fridtjof (author), Pawlik, G. (author), Halatek, Jacob (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological processes inherently involve multiple spatial and temporal scales and transition from one pattern to another...journal article 2022
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Satam, Anuja P. (author), van der Leeden, Marike (author), de Zwart, Arjan (author), Verberne, Simon (author), Schrijvers, Jim C. (author), Hall, Michelle (author), Dekker, Joost (author), Lems, Willem F. (author), Harlaar, J. (author), van der Esch, Martin (author)Background: Muscle weakness is characteristic of knee osteoarthritis. Muscle steadiness may be an important adjunct to knee muscle strength in improving physical function in knee osteoarthritis. However, the role of muscle steadiness is uncertain. Aims: To determine the associations of knee extensor muscle steadiness with maximal voluntary...journal article 2022
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Boskeljon-Horst, L. (author), Sillem, S. (author), Dekker, S.W.A. (author)There is little empirical evidence on the predictive value of safety culture assessments (SCAs) in relation to how accident-prone an organisation might be. Recently, Antonsen not just demonstrated how a quantitative SCA mispredicted future safety outcomes, but actually showed an inverse relationship between the assessment and subsequent critical...journal article 2022
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Dekker, S.W.A. (author), Layson, Mark D. (author), Woods, David D. (author)Following other contributions about the MAX accidents to this journal, this paper explores the role of betrayal and moral injury in safety engineering related to the U.S. federal regulator’s role in approving the Boeing 737MAX—a plane involved in two crashes that together killed 346 people. It discusses the tension between humility and hubris...journal article 2022
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de Haas, K. (author), Berkhout, B (author), Dekker, H.R.E. (author), Broere, W. (author)Determining the scope of (structural) renovation of aging tunnels is a complicated task and modular renovation is becoming increasingly necessary. The COB Tunnel Programme aims at developing the knowledge necessary to renovate these tunnels in a modular fashion, to reduce hindrance as much as possible. Part of this program is the development of...conference paper 2022
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Li, J. (author), Li, Chenhui (author), Henneken, Vincent (author), Louwerse, Marcus (author), Van Rens, Jeannet (author), Dijkstra, Paul (author), Raz, Oded (author), Dekker, R. (author)The digitization of smart catheters will dramatically increase the demand for reliable and high data transmission in the distal tips. Optical fiber is a good candidate to provide high-speed data transmission. However, the extremely small size of the smart catheter tip, with less than a few millimeters in diameter, hampers the integration of...journal article 2022
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Whitley, K.D. (author), Middlemiss, Stuart (author), Jukes, Calum (author), Dekker, C. (author), Holden, Séamus (author)Light microscopy is indispensable for analysis of bacterial spatial organization, yet the sizes and shapes of bacterial cells pose unique challenges to imaging. Bacterial cells are not much larger than the diffraction limit of visible light, and many species have cylindrical shapes and so lie flat on microscope coverslips, yielding low...review 2022
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Blanch Jover, A. (author), De Franceschi, N. (author), Fenel, Daphna (author), Weissenhorn, Winfried (author), Dekker, C. (author)The Cdv proteins constitute the cell division system of the Crenarchaea, a machinery closely related to the ESCRT system of eukaryotes. Using a combination of TEM imaging and biochemical assays, we here present an in vitro study of Metallosphaera sedula CdvB1, the Cdv protein that is believed to play a major role in the constricting ring that...journal article 2022
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Roslon, I.E. (author), Japaridze, A. (author), Steeneken, P.G. (author), Dekker, C. (author), Alijani, F. (author)Motion is a key characteristic of every form of life<sup>1</sup>. Even at the microscale, it has been reported that colonies of bacteria can generate nanomotion on mechanical cantilevers<sup>2</sup>, but the origin of these nanoscale vibrations has remained unresolved<sup>3,4</sup>. Here, we present a new technique using drums made of...journal article 2022
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Dekker, J.J. (author), van Dongen, Jacques J.M. (author), Reinders, M.J.T. (author), Khatri, Indu (author)The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information...journal article 2022
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Shi, X. (author), Pumm, Anna Katharina (author), Isensee, Jonas (author), Zhao, W. (author), Verschueren, D.V. (author), Martin Gonzalez, A. (author), Golestanian, Ramin (author), Dietz, Hendrik (author), Dekker, C. (author)Flow-driven rotary motors such as windmills and water wheels drive functional processes in human society. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has remained challenging. Here we demonstrate flow-driven rotary motion of a self-organized DNA nanostructure...journal article 2022
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Ying, Yi Lun (author), Hu, Zheng Li (author), Zhang, Shengli (author), Qing, Yujia (author), Fragasso, A. (author), Maglia, Giovanni (author), Meller, Amit (author), Bayley, Hagan (author), Dekker, C. (author), Long, Yi Tao (author)Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the...review 2022
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Dekker, H.N.J. (author), Ragni, D. (author), Baars, W.J. (author), Scarano, F. (author), Tuinstra, Marthijn (author)An experimental investigation is conducted to study the aerodynamic behavior of a two-rotor system in ground proximity. The counter-rotating rotors are placed side-by-side in the hovering condition. The time-averaged and unsteady flow behavior is studied when the rotor-to-rotor lateral distance and the distance between the rotors and the...journal article 2022
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Wen, C. (author), Bertosin, E. (author), Shi, X. (author), Dekker, C. (author), Schmid, Sonja (author)Nanopores are versatile single-molecule sensors offering a simple label-free readout with great sensitivity. We recently introduced the nanopore electro-osmotic trap (NEOtrap) which can trap and sense single unmodified proteins for long times. The trapping is achieved by the electro-osmotic flow (EOF) generated from a DNA-origami sphere...journal article 2022
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Janissen, R. (author), Eslami Mossallam, B. (author), Artsimovitch, Irina (author), Depken, S.M. (author), Dekker, N.H. (author)Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our mechanistic understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high...journal article 2022
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Bengtson, M.L. (author), Bharadwaj, M. (author), Franch, O. (author), van der Torre, J. (author), Meerdink, V.E.E. (author), Schallig, Henk (author), Dekker, C. (author)Nucleic-acid detection is crucial for basic research as well as for applications in medicine such as diagnostics. In resource-limited settings, however, most DNA-detection diagnostic schemes are inapplicable since they rely on expensive machinery, electricity, and trained personnel. Here, we present an isothermal DNA detection scheme for the...journal article 2022