- document
-
Restrepo Sierra, A.M. (author)Life, the most complex and admirable machine that one could think of has evolved over billions of years to display a beautiful variety of mechanisms that keep cells adapting, self-maintaining, reproducing, and evolving. If we think about it, what is this magic? What are the mechanisms behind life’s origins and wonderful coordination? Attracted...doctoral thesis 2024
- document
-
Hoencamp, C. (author)Every human being originates from a single fertilized egg cell, continuously duplicating to form a body consisting of trillions of cells in a process known as the cell cycle. This cycle involves two major stages: interphase, where the cell prepares for division, and mitosis, where it divides into two daughter cells. The accurate duplication and...doctoral thesis 2024
- document
-
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
- document
-
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
- document
-
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
- document
-
Hijaze, Eman (author), Gildor, Tsvia (author), Seidel, Ronald (author), Layous, Majed (author), Winter, M.R. (author), Bertinetti, Luca (author), Politi, Yael (author), Ben-Tabou de-Leon, Smadar (author)Biomineralization had apparently evolved independently in different phyla, using distinct minerals, organic scaffolds, and gene regulatory networks (GRNs). However, diverse eukaryotes from unicellular organisms, through echinoderms to vertebrates, use the actomyosin network during biomineralization. Specifically, the actomyosin remodeling...journal article 2024
- document
-
Shomar, Helena (author), Bokinsky, G.E. (author)Reactions catalysed by iron-sulfur (Fe-S) enzymes appear in a variety of biosynthetic pathways that produce valuable natural products. Harnessing these biosynthetic pathways by expression in microbial cell factories grown on an industrial scale would yield enormous economic and environmental benefits. However, Fe-S enzymes often become...review 2024
- document
-
Koster, C.C. (author)Building synthetic cells is extremely interesting from a fundamental perspective, as the ability to rationally build viable, dividing, and self-maintaining cells provides knowledge on the minimal requirements to sustain life. This should enhance our understanding about which biological parts are minimally required for a cell to live, and how...doctoral thesis 2023
- document
-
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
- document
-
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
- document
-
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
- document
-
Van de Cauter, L. (author), van Buren, L. (author), Koenderink, G.H. (author), Ganzinger, Kristina A. (author)Creating an artificial cell from the bottom up is a long-standing challenge and, while significant progress has been made, the full realization of this goal remains elusive. Arguably, one of the biggest hurdles that researchers are facing now is the assembly of different modules of cell function inside a single container. Giant unilamellar...review 2023
- document
-
Filius, M. (author), van Wee, R.G. (author), Joo, C. (author)Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short...book chapter 2023
- document
-
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
- document
-
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
- document
-
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
- document
-
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
- document
-
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
- document
-
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
- document
-
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