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Kim, Eugene (author), Barth, R. (author), Dekker, C. (author)SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes play a key role in a variety of functions in the packaging and regulation of chromosomes, and they have...review 2023
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Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical NanoporesKlughammer, N. (author), Barth, A. (author), Dekker, Maurice (author), Fragasso, A. (author), Onck, Patrick R. (author)The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single...journal article 2023
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Shi, X. (author), Pumm, Anna Katharina (author), Maffeo, Christopher (author), Kohler, Fabian (author), Feigl, Elija (author), Zhao, W. (author), Verschueren, D.V. (author), Golestanian, Ramin (author), Aksimentiev, Aleksei (author), Dietz, Hendrik (author), Dekker, C. (author)Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA...journal article 2023
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Meindlhumer, S. (author), Brauns, Fridtjof (author), Finžgar, Jernej Rudi (author), Kerssemakers, J.W.J. (author), Dekker, C. (author), Frey, Erwin (author)The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD...journal article 2023
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De Franceschi, N. (author), Barth, R. (author), Meindlhumer, S. (author), Fragasso, A. (author), Dekker, C. (author)Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division and in other cellular processes such as endocytosis, virus release or bacterial sporulation. However, its mechanism remains poorly understood, impeding its application as a cell-division...journal article 2023
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Barth, R. (author), Pradhan, B. (author), Kim, E. (author), Davidson, Iain F. (author), van der Torre, J. (author), Peters, Jan Michael (author), Dekker, C. (author)DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The ring-like structure of SMC complexes prompted multiple models where the extruded DNA is topologically or...journal article 2023
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A new setup to study the influence of plant growth on the consolidation of dredged cohesive sedimentBarciela Rial, M. (author), Saaltink, Remon M. (author), van Kessel, Thijs (author), Chassagne, C. (author), Dekker, Stefan C. (author), de Boer, Hugo J. (author), Griffioen, Jasper (author), Wassen, Martin J. (author), Winterwerp, J.C. (author)Dredged cohesive sediment is progressively being used for wetland construction. However, little is known about the effect of plant growth during the self-weight consolidation of this sediment. In order to check the feasibility of such a study, a new experimental setup has been constructed. As an example, the effect of Phragmites australis on the...journal article 2023
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Dekker, H.N.J. (author), Baars, W.J. (author), Scarano, F. (author), Tuinstra, Marthijn (author), Ragni, D. (author)The unsteady flow behaviour of two side-by-side rotors in ground proximity is experimentally investigated. The rotors induce a velocity distribution interacting with the ground causing the radial expansion of the rotor wakes. In between the rotors, an interaction of the two wakes takes place, resulting in an upward flow similar to a fountain....journal article 2023
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Japaridze, A. (author), van Wee, R.G. (author), Gogou, C. (author), Kerssemakers, J.W.J. (author), van den Berg, D.F. (author), Dekker, C. (author)The bacterial chromosome is spatially organized through protein-mediated compaction, supercoiling, and cell-boundary confinement. Structural Maintenance of Chromosomes (SMC) complexes are a major class of chromosome-organizing proteins present throughout all domains of life. Here, we study the role of the Escherichia coli SMC complex MukBEF...journal article 2023
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Nova, I.C. (author), Ritmejeris, J. (author), Brinkerhoff, H.D. (author), Koenig, T.J.R. (author), Gundlach, Jens H. (author), Dekker, C. (author)Current methods to detect post-translational modifications of proteins, such as phosphate groups, cannot measure single molecules or differentiate between closely spaced phosphorylation sites. We detect post-translational modifications at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants by...journal article 2023
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Yang, Sora (author), Klughammer, N. (author), Barth, A. (author), Tanenbaum, M. (author), Dekker, C. (author)Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic...journal article 2023
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Roslon, I.E. (author), Japaridze, A. (author), Rodenhuis, Stef (author), Hamoen, Lieke (author), Ghatkesar, M.K. (author), Steeneken, P.G. (author), Dekker, C. (author), Alijani, F. (author)Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The...journal article 2023
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Dekker, Mark M. (author), Daioglou, Vassilis (author), Pietzcker, Robert (author), Rodrigues, Renato (author), de Boer, Harmen Sytze (author), Dalla Longa, Francesco (author), Drouet, Laurent (author), Emmerling, Johannes (author), Fattahi, Amir (author), Fotiou, Theofano (author), Fragkos, Panagiotis (author), Fricko, Oliver (author), Gusheva, E. (author), Harmsen, Mathijs (author), Huppmann, Daniel (author), Kannavou, Maria (author), Krey, Volker (author), Lombardi, F. (author), Luderer, Gunnar (author), Pfenninger, Stefan (author), Tsiropoulos, Ioannis (author), Zakeri, Behnam (author), van der Zwaan, Bob (author), Usher, Will (author), van Vuuren, Detlef (author)Energy models are used to study emissions mitigation pathways, such as those compatible with the Paris Agreement goals. These models vary in structure, objectives, parameterization and level of detail, yielding differences in the computed energy and climate policy scenarios. To study model differences, diagnostic indicators are common practice...journal article 2023
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Rouillon, Clément (author), Eckhardt, Bruna V. (author), Kollenstart, Leonie (author), Gruss, Fabian (author), Verkennis, Alexander E.E. (author), Rondeel, Inge (author), van Laar, T. (author), Albanese, Pascal (author), Dekker, N.H. (author)During every cell cycle, both the genome and the associated chromatin must be accurately replicated. Chromatin Assembly Factor-1 (CAF-1) is a key regulator of chromatin replication, but how CAF-1 functions in relation to the DNA replication machinery is unknown. Here, we reveal that this crosstalk differs between the leading and lagging...journal article 2023
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Mc Cluskey, K.A. (author), Dekker, N.H. (author)TIRF (Total Internal Reflection Fluorescence) microscopy is a powerful tool for measuring the intra- and intermolecular dynamics of fluorescently-labeled single molecules. As TIRF measurements move to more complex biological systems with more fluorescent probes, the multi-band-pass dichroic that separates excitation from emission becomes...journal article 2023
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Davidson, Iain F. (author), Barth, R. (author), Zaczek, Maciej (author), van der Torre, J. (author), Tang, Wen (author), Nagasaka, Kota (author), Janissen, R. (author), Kerssemakers, J.W.J. (author), Wutz, Gordana (author), Dekker, C. (author), Peters, Jan Michael (author)In eukaryotes, genomic DNA is extruded into loops by cohesin<sup>1</sup>. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)<sup>2,3</sup> that have important roles in gene regulation and recombination during development and disease<sup>1,4–7</sup>. How CTCF...journal article 2023
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Ramirez Montero, D.F. (author), Sanchez González, H. (author), van Veen, E.N.W. (author), van Laar, T. (author), Solano Hermosilla, B.P. (author), Diffley, John F.X. (author), Dekker, N.H. (author)The eukaryotic replicative helicase CMG centrally orchestrates the replisome and leads the way at the front of replication forks. Understanding the motion of CMG on the DNA is therefore key to our understanding of DNA replication. In vivo, CMG is assembled and activated through a cell-cycle-regulated mechanism involving 36 polypeptides that...journal article 2023
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He, P. (author), Katan, A.J. (author), Tubiana, Luca (author), Dekker, C. (author), Michieletto, Davide (author)Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked DNA minicircles found in certain parasites called trypanosomes. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials. Here, we...journal article 2023
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Dekker, C. (author), Haering, Christian H. (author), Peters, Jan Michael (author), Rowland, B.D. (author)A potential mechanism of DNA loop extrusion by molecular motors is discussed.journal article 2023
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Dekker, Bo (author), Schouten, A.C. (author), Scharenborg, O.E. (author)Silent speech interfaces could enable people who lost the ability to use their voice or gestures to communicate with the external world, e.g., through decoding the person’s brain signals when imagining speech. Only a few and small databases exist that allow for the development and training of brain computer interfaces (BCIs) that can decode...conference paper 2023