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Godino, E. (author), Danelon, C.J.A. (author)Mimicking bacterial cell division in well-defined cell-free systems has the potential to elucidate the minimal set of proteins required for cytoskeletal formation, membrane constriction, and final abscission. Membrane-anchored FtsZ polymers are often regarded as a sufficient system to realize this chain of events. By using purified FtsZ and...journal article 2023
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Aldulijan, Ibrahim (author), Beal, Jacob (author), Billerbeck, Sonja (author), Bouffard, Jeff (author), Chambonnier, Gaël (author), Ntelkis, Nikolaos (author), Guerreiro, Isaac (author), Holub, M. (author), Ross, Paul (author)Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms. However, current paradigms in the field entangle sequence and functionality in a manner that makes...review 2023
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Forman, Jack (author), Pataranutaporn, Pat (author), Gough, Phillip (author), Kim, Raphael (author), Bell, Fiona (author), Ofer, Netta (author), Lu, Jasmine (author), Vujic, Angela (author), Bai, Muqing (author)As knowledge around bio-digital interaction continues to unfold, there are new opportunities for HCI researchers to integrate biology as a design and computational material. Our motivation for the workshop is to bring together interdisciplinary researchers with interest in exploring the next generation of biological HCI and exploring novel...conference paper 2023
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van Vroonhoven, Thomas (author)This project models collective cell migration and differentiation as part of a wound healing process. The hybrid mathematical model used in this project consists of an agent-based model for the cells combined with a system of coupled partial differential equations for two forms of the growth factor molecule TGF-beta. The model is implemented in...bachelor thesis 2022
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Laman Trip, J.D.S. (author)Open questions are whether life can be enabled in uninhabitable environments, and whether there is a limit to howmuch one can tune the speed of proliferation. Answering such questions has broad implications. It may reveal whether we can live in unforeseen habitats, whether we can slow down aging, and whether there are limits to lifespan. In this...doctoral thesis 2022
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Godino, E. (author)The Christophe Danelon lab is involved in the long-term effort to construct an autonomous minimal cell using a bottom-up approach. Our goal is to achieve self-maintenance, selfreproduction, and evolution of a liposome compartment containing a minimal genome and a cell-free gene expression system. Self-reproduction requires splitting of the...doctoral thesis 2022
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van Aalst, A.C.A. (author), de Valk, S.C. (author), van Gulik, W.M. (author), Jansen, Mickel L.A. (author), Pronk, J.T. (author), Mans, R. (author)Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth...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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Boonekamp, F.J. (author), Knibbe, E. (author), Vieira Lara, M.A. (author), Wijsman, M. (author), Luttik, M.A.H. (author), van Eunen, Karen (author), den Ridder, M.J. (author), Pabst, Martin (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single...journal article 2022
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Severins, I.W.H. (author), Joo, C. (author), van Noort, John (author)Next-generation sequencing techniques have led to a new quantitative dimension in the biological sciences. In particular, integrating sequencing techniques with biophysical tools allows sequence-dependent mechanistic studies. Using the millions of DNA clusters that are generated during sequencing to perform high-throughput binding affinity...review 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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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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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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D'Angelo, Francesca (author), Fernandez Fueyo, E. (author), Garcia, Pierre Simon (author), Shomar Monges, H. (author), Cebola Rebelo Manuel, R.S. (author), Büke, F. (author), van den Broek, N.J.F. (author), de Ram, C. (author), Pabst, Martin (author)Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and distributed to Fe-S enzymes by dedicated protein networks. The core components of these networks are widely conserved and highly versatile. However, Fe-S proteins and...journal article 2022
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Mashaghi, Alireza (author), Moayed, Fatemeh (author), Koers, Eline J. (author), Zheng, Yang (author), Till, K. (author), Kramer, Günter (author), Mayer, Matthias P. (author), Tans, S.J. (author)The chaperone heat shock protein 90 (Hsp90) is well known to undergo important conformational changes, which depend on nucleotide and substrate interactions. Conversely, how the conformations of its unstable and disordered substrates are affected by Hsp90 is difficult to address experimentally yet is central to its function. Here, using...journal article 2022
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Minden, Steven (author), Aniolek, Maria (author), Sarkizi Shams Hajian, Christopher (author), Teleki, Attila (author), Zerrer, Tobias (author), Delvigne, Frank (author), van Gulik, W.M. (author), Deshmukh, Amit (author), Noorman, H.J. (author), Takors, Ralf (author)Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and...journal article 2022
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Vrijhof, Michaël (author)From a biological perspective, I have researched how our bodies have evolved in the biosphere for millions of years and therefore we are wired to have an incredibly rich diet of sensory stimuli. I have distinguished some of our intrinsic needs, and accompanied them with the latest design tools from the field of environmental psychology and neuro...master thesis 2021
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Daneshpour Aryadi, H. (author)Tales of a Fountain of Youth and the invention of medicine illustrate our age-long obsession with two themes: life and death. What it takes to stay alive, and not to be dead, is a basic question in science that is easy to state, and yet difficult to address at a profound level. One striking feature of many living organisms is the ability of...doctoral thesis 2021
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- Janssen, R. (author) doctoral thesis 2021
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Makrodimitris, S. (author)Billions of people world-wide rely on plant-based food for their daily energy intake. As global warming and the spread of diseases (such as the banana Panama disease) is substantially hindering the cultivation of plants, the need to develop temperature- and/or disease-resistant varieties is getting more and more pressing. The field of plant...doctoral thesis 2021