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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
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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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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
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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
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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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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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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
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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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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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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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Blanken, D.M. (author)Cells, the building blocks of life, are vastly complex. This complexity confers to every living organism the ability to maintain oneself, reproduce oneself, and evolve. Creating a minimal system from nonliving components that is capable of self-maintenance, self-reproduction, and evolvability, will greatly increase our understanding of life....doctoral thesis 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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Shomar, Helena (author), Bokinsky, G.E. (author)Microbes are routinely engineered to synthesize high-value chemicals from renewable materials through synthetic biology and metabolic engineering. Microbial biosynthesis often relies on expression of heterologous biosynthetic pathways, i.e., enzymes transplanted from foreign organisms. Metallocluster enzymes are one of the most ubiquitous...review 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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Kattan, J.M. (author)Humanity has achieved to decipher the most fundamental mechanics of cellular life. Nevertheless, despite intense efforts there are still considerable gaps in our understanding of cellular processes. Traditionally, biologists investigate life by observation of existing lifeforms. In order to assign functions to biological components, it is common...doctoral thesis 2020
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Abil, Z. (author), Danelon, C.J.A. (author)Laboratory synthesis of an elementary biological cell from isolated components may aid in understanding of the fundamental principles of life and will provide a platform for a range of bioengineering and medical applications. In essence, building a cell consists in the integration of cellular modules into system’s level functionalities...journal article 2020
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Bruynseels, K.R.C. (author)Synthetic biology, as an engineering approach to biological systems, has the potential to disruptively innovate the development of vaccines, therapeutics, and diagnostics. Data accessibility and differences in data-usage capabilities are important factors in shaping this innovation landscape. In this paper, the data that underpin synthetic...journal article 2020
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Noguera López, J. (author)The creation of artificial cells with the minimal set of components to exhibit self-maintenance, self-reproducibility and evolvability (in other words, to be considered alive) is one of the most exciting areas within the field of synthetic biology. Such entities, here called minimal cells, are constructed by either the top-down or bottom-up...doctoral thesis 2019
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Soler Canton, A. (author)Synthetic biology is an emerging and rapidly expanding field of research focused on the assembly of novel biological systems with new functionalities tailored for different applications. Genetic circuits have been re-wired or constructed with elements from different organisms, and metabolic pathways have been engineered to endow cells with non...doctoral thesis 2019
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