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Fayezioghani, A. (author), Dekker, R. (author), Sluys, Lambertus J. (author)Corrosion is a phenomenon observed in structural components in corrosive environments such as pipelines, bridges, aircrafts, turbines, etc. The computational model of corrosion should enjoy two features: a) accurately considering the electrochemistry of corrosion and b) properly dealing with the moving interface between solid and electrolyte....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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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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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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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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Mc Cluskey, K.A. (author), van Veen, E.N.W. (author), Cnossen, J.P. (author), Wesselink, W.J. (author), Asscher, F.M. (author), Smith, C.S. (author), Dekker, N.H. (author)Accurate image alignment is critical in multicolor single-molecule fluorescence microscopy. Global alignment using affine transformations leaves residual errors due to the nonlinearity of the distortions, which decreases the effective field of view. Subsequent local refinement demands either large amounts of reference data and processing time...journal article 2021
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Kluba, M.M. (author), Li, J. (author), Parkkinen, Katja (author), Louwerse, Marcus (author), Snijder, Jaap (author), Dekker, R. (author)Several Silicon on Insulator (SOI) wafer manufacturers are now offering products with customer‐defined cavities etched in the handle wafer, which significantly simplifies the fabrication of MEMS devices such as pressure sensors. This paper presents a novel cavity buried oxide (BOX) SOI substrate (cavity‐BOX) that contains a patterned BOX...journal article 2021
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Dekker, Mireille (author), de Koning, Judith PM (author), Melles, M. (author), Sonneveld, M.H. (author), van Mansfeld, Rosa (author), Jongerden, Irene P (author)Background: Patient information provision about isolation measures is often not standardized. Moreover, it is unclear what information patients and informal caregivers need to optimize their knowledge and actual experience of contact isolation. We explored opportunities for improving the experience of patients in contact isolation from a human...journal article 2021
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Dekker, M.C. (author), van Egmond, R. (author), Molenbroek, J.F.M. (author), Vink, P. (author)BACKGROUND: Former studies on work-related upper limb disorders (WRULD) within university education report substantial prevalence rates. In this study, developments in WRULD amongst students in the period 2004-2014 were investigated. Our findings can be a benchmark for future studies, in particular when there are major societal changes as in...journal article 2021
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Mooiman, C. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Ortiz Merino, R.A. (author), de Hulster, A.F. (author), Pronk, J.T. (author)All known facultatively fermentative yeasts require molecular oxygen for growth. Only in a small number of yeast species, these requirements can be circumvented by supplementation of known anaerobic growth factors such as nicotinate, sterols and unsaturated fatty acids. Biosynthetic oxygen requirements of yeasts are typically small and,...journal article 2021
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Perli, T. (author), Vos, A.M. (author), Bouwknegt, J. (author), Dekker, W.J.C. (author), Wiersma, S.J. (author), Mooiman, C. (author), Ortiz Merino, R.A. (author), Daran, J.G. (author), Pronk, J.T. (author)Neocallimastigomycetes are unique examples of strictly anaerobic eukaryotes. This study investigates how these anaerobic fungi bypass reactions involved in synthesis of pyridine nucleotide cofactors and coenzyme A that, in canonical fungal pathways, require molecular oxygen. Analysis of Neocallimastigomycetes proteomes identified a candidate...journal article 2021
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Hulleman, C.N. (author), Thorsen, R.Ø. (author), Kim, E. (author), Dekker, C. (author), Stallinga, S. (author), Rieger, B. (author)Estimating the orientation and 3D position of rotationally constrained emitters with localization microscopy typically requires polarization splitting or a large engineered Point Spread Function (PSF). Here we utilize a compact modified PSF for single molecule emitter imaging to estimate simultaneously the 3D position, dipole orientation, and...journal article 2021
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Fragasso, A. (author), de Vries, Hendrik W. (author), Andersson, John (author), van der Sluis, E.O. (author), van der Giessen, Erik (author), Dahlin, Andreas (author), Onck, Patrick R. (author), Dekker, C. (author)Nuclear Pore Complexes (NPCs) regulate bidirectional transport between the nucleus and the cytoplasm. Intrinsically disordered FG-Nups line the NPC lumen and form a selective barrier, where transport of most proteins is inhibited whereas specific transporter proteins freely pass. The mechanism underlying selective transport through the NPC is...journal article 2021
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Martins Da Ponte, R. (author), Gaio, N. (author), van Zeijl, H.W. (author), Vollebregt, S. (author), Dijkstra, Paul (author), Dekker, R. (author), Serdijn, W.A. (author), Giagka, Vasiliki (author)One of the many applications of organ-on-a-chip (OOC) technology is the study of biological processes in human induced pluripotent stem cells (iPSCs) during pharmacological drug screening. It is of paramount importance to construct OOCs equipped with highly compact in situ sensors that can accurately monitor, in real time, the extracellular...journal article 2021
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Yang, W.W.W. (author), van Dijk, M.C. (author), Primavera, Christian (author), Dekker, C. (author)We have developed a fabrication methodology for label-free optical trapping of individual nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of these nanoapertures can be reliably produced using focused ion beam (FIB) milling with gap sizes of 10–20 nm, single-nanometer variation, and with a remarkable stability...journal article 2021
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Janissen, R. (author), Woodman, Andrew (author), Shengjuler, Djoshkun (author), Vallet, Thomas (author), Lee, Kuo Ming (author), Kuijpers, L.C. (author), Moustafa, Ibrahim M. (author), Fitzgerald, Fiona (author), Dekker, N.H. (author)Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics...journal article 2021
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Van de Cauter, L. (author), Fanalista, F. (author), van Buren, L. (author), De Franceschi, N. (author), Godino, E. (author), Bouw, Sharon (author), Danelon, C.J.A. (author), Dekker, C. (author), Koenderink, G.H. (author), Ganzinger, Kristina A. (author)Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to...journal article 2021
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Fragasso, A. (author), De Franceschi, N. (author), Stömmer, Pierre (author), van der Sluis, E.O. (author), Dietz, Hendrik (author), Dekker, C. (author)Molecular traffic across lipid membranes is a vital process in cell biology that involves specialized biological pores with a great variety of pore diameters, from fractions of a nanometer to >30 nm. Creating artificial membrane pores covering similar size and complexity will aid the understanding of transmembrane molecular transport in...journal article 2021