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Holub, M. (author), Birnie, A.T.F. (author), Japaridze, A. (author), van der Torre, J. (author), Ridder, Maxime den (author), de Ram, C. (author), Pabst, Martin (author), Dekker, C. (author)Chromosome structure and function is studied using various cell-based methods as well as with a range of in vitro single-molecule techniques on short DNA substrates. Here, we present a method to obtain megabase-pair-length deproteinated DNA for in vitro studies. We isolated chromosomes from bacterial cells and enzymatically digested the...journal article 2022
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Dekker, W.J.C. (author), Jürgens, H. (author), Ortiz Merino, R.A. (author), Mooiman, C. (author), van den Berg, Remon (author), Kaljouw, Astrid (author), Mans, R. (author), Pronk, J.T. (author)While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha...journal article 2022
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Kuijpers, L.C. (author), van Laar, T. (author), Janissen, R. (author), Dekker, N.H. (author)Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing...journal article 2022
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Kim, E. (author), Martin Gonzalez, A. (author), Pradhan, B. (author), van der Torre, J. (author), Dekker, C. (author)Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, for example, the torsional stresses that are generated by other DNA-processing enzymes. It has so far...journal article 2022
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Dekker, S.W.A. (author), Tooma, Michael (author)The shortcomings of incident-based metrics for worker safety such as total recordable incident frequency rate (TRIFR) are well documented. In particular, a low TRIFR is no assurance against legal liability. There is considerable overlap between the literature on safety as the presence of capacities to make things go well, and jurisprudence in...journal article 2022
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Meindlhumer, S. (author), Kerssemakers, J.W.J. (author), Dekker, C. (author)The Min protein system is arguably the best-studied model system for biological pattern formation. It exhibits pole-to-pole oscillations in E. coli bacteria as well as a variety of surface wave patterns in in vitro reconstitutions. Such Min surface wave patterns pose particular challenges to quantification as they are typically only semi...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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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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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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Pradhan, B. (author), Barth, R. (author), Kim, E. (author), van Laar, T. (author), Yang, W.W.W. (author), Ryu, J.K. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro single-molecule visualization to show that nucleosomes, RNA polymerase, and dCas9 pose virtually no...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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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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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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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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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, 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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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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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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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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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