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Directing Min protein patterns with advective bulk flow

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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A new setup to study the influence of plant growth on the consolidation of dredged cohesive sediment

Barciela 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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Opto-electronic feedback control of membrane potential for real-time control of action potentials

Ördög, Balázs (author), De Coster, Tim (author), Dekker, Sven O. (author), Bart, Cindy I. (author), Zhang, Juan (author), Boink, Gerard J.J. (author), Bax, Wilhelmina H. (author), Deng, Shanliang (author), den Ouden, B.L. (author), de Vries, Antoine A.F. (author), Pijnappels, Daniël A. (author)

To unlock new research possibilities by acquiring control of action potential (AP) morphologies in excitable cells, we developed an opto-electronic feedback loop-based system integrating cellular electrophysiology, real-time computing, and optogenetic approaches and applied it to monolayers of heart muscle cells. This allowed accurate...

journal article 2023

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Dynamin A as a one-component division machinery for synthetic cells

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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CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion

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 cohesin¹. By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs)^2,3 that have important roles in gene regulation and recombination during development and disease^1,4–7. How CTCF...

journal article 2023

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Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments

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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Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation

Tišma, M. (author), Janissen, R. (author), Antar, Hammam (author), Martin Gonzalez, A. (author), Barth, R. (author), Beekman, T.G.T. (author), van der Torre, J. (author), Michieletto, Davide (author), Gruber, Stephan (author), Dekker, C. (author)

In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex for Bacillus subtilis ParB, using single-molecule fluorescence microscopy and AFM imaging to show that...

journal article 2023

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Unsteady flow behaviour of multi-rotors in ground proximity

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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Healthy computer working

Dekker, M.C. (author)

Repetitive Strain Injuries (RSI), also known as Work-Related Upper Limb Disorders (WRULD), surged in the early years of this millennium due to computer work. In this thesis, the magnitude, causes and consequences of this phenomenon for the student population of the Faculty of Industrial Design Engineering (IDE) at the Delft University of...

doctoral thesis 2022

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A Microfluidic Cancer-on-Chip Platform Predicts Drug Response Using Organotypic Tumor Slice Culture

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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Focused ultrasound neuromodulation on a multiwell MEA

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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The associations of knee extensor muscle steadiness with maximal voluntary torque and physical function in patients with knee osteoarthritis

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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‘Ladder’-based safety culture assessments inversely predict safety outcomes

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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Managing Knowledge for Future-proof Tunnels in the Netherlands

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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The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC

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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Probing nanomotion of single bacteria with graphene drums

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 life¹. Even at the microscale, it has been reported that colonies of bacteria can generate nanomotion on mechanical cantilevers², but the origin of these nanoscale vibrations has remained unresolved^3,4. Here, we present a new technique using drums made of...

journal article 2022

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pmTR database: Population matched (pm) germline allelic variants of T-cell receptor (TR) loci

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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Sustained unidirectional rotation of a self-organized DNA rotor on a nanopore

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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Nanopore-based technologies beyond DNA sequencing

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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Orientation-Locked DNA Origami for Stable Trapping of Small Proteins in the Nanopore Electro-Osmotic Trap

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