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Slijkhuis, Nuria (author), Razzi, F. (author), Korteland, Suze Anne (author), Heijs, Bram (author), van Gaalen, Kim (author), Duncker, Dirk J. (author), van der Steen, A.F.W. (author), van Steijn, V. (author), van Beusekom, Heleen M.M. (author), van Soest, G. (author)Coronary atherosclerosis is caused by plaque build-up, with lipids playing a pivotal role in its progression. However, lipid composition and distribution within coronary atherosclerosis remain unknown. This study aims to characterize lipids and investigate differences in lipid composition across disease stages to aid in the understanding of...journal article 2024
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Jaroensuk, Juthamas (author), Sutthaphirom, Chalermroj (author), Phonbuppha, Jittima (author), Chinantuya, Wachirawit (author), Kesornpun, Chatchai (author), Akeratchatapan, Nattanon (author), Kittipanukul, Narongyot (author), Phatinuwat, Kamonwan (author), Hollmann, F. (author)Cofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system...journal article 2024
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Huber, Katharina T. (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, V.L. (author), Murakami, Yukihiro (author), Semple, Charles (author)This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network....journal article 2024
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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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Noom, J. (author), Smith, C.S. (author), Verbiest, G.J. (author), Katan, A.J. (author), Soloviev, O.A. (author), Verhaegen, M.H.G. (author)We propose to use the State Estimation by Sum-of-Norms Regularisation (STATESON-)algorithm for recovering the tip-sample interaction in high-speed tapping mode atomic force microscopy (AFM). This approach enables accurate sample height estimation for each independent cantilever oscillation period, provided that the tip-sample interaction...journal article 2023
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Novella-Rausell, Claudio (author), Grudniewska, Magda (author), Peters, Dorien J.M. (author), Mahfouz, A.M.E.T.A. (author)The kidney's cellular diversity is on par with its physiological intricacy; yet identifying cell populations and their markers remains challenging. Here, we created a comprehensive atlas of the healthy adult mouse kidney (MKA: Mouse Kidney Atlas) by integrating 140.000 cells and nuclei from 59 publicly available single-cell and single-nuclei...journal article 2023
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Wehrens, Martijn (author), Krah, Laurens H.J. (author), Towbin, Benjamin D. (author), Hermsen, Rutger (author), Tans, S.J. (author)The inherent stochasticity of metabolism raises a critical question for understanding homeostasis: are cellular processes regulated in response to internal fluctuations? Here, we show that, in E. coli cells under constant external conditions, catabolic enzyme expression continuously responds to metabolic fluctuations. The underlying...journal article 2023
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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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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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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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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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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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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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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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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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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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Ju, Jie (author), Wismans, Leonoor V. (author), Mustafa, Dana A.M. (author), Reinders, M.J.T. (author), van Eijck, Casper H.J. (author), Li, Yunlei (author)A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder...journal article 2021
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Balasubramanian, S. (author), Yu, K. (author), Vasquez Cardenas, D. (author), Aubin-Tam, M.E. (author), Meyer, Anne S. (author)Biofilms are three-dimensional (3D) bacterial communities that exhibit a highly self-organized nature in terms of their composition and complex architecture. Bacteria in biofilms display emergent biological properties, such as resistance to antimicrobials and disinfectants that the individual planktonic cells lack. Bacterial biofilms possess...journal article 2021
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Sarkar, A. (author), Al-Ars, Z. (author), Bertels, K.L.M. (author)Inferring algorithmic structure in data is essential for discovering causal generative models. In this research, we present a quantum computing framework using the circuit model, for estimating algorithmic information metrics. The canonical computation model of the Turing machine is restricted in time and space resources, to make the target...journal article 2021
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de Lannoy, C.V. (author), Filius, M. (author), van Wee, R.G. (author), Joo, C. (author), de Ridder, Dick (author)Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and...journal article 2021