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Páez Watson, T.W. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic...
journal article 2024
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Páez Watson, T.W. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
The understanding of microbial communities and the biological regulation of its members is crucial for implementation of novel technologies using microbial ecology. One poorly understood metabolic principle of microbial communities is resource allocation and biosynthesis. Resource allocation theory in polyphosphate accumulating organisms ...
journal article 2023
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Lao-Martil, David (author), Verhagen, K.J.A. (author), Valdeira Caetano, Ana H. (author), Pardijs, Ilse H. (author), van Riel, Natal A.W. (author), Wahl, S.A. (author)
Microbial metabolism is strongly dependent on the environmental conditions. While these can be well controlled under laboratory conditions, large-scale bioreactors are characterized by inhomogeneities and consequently dynamic conditions for the organisms. How Saccharomyces cerevisiae response to frequent perturbations in industrial...
journal article 2023
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Soares Rodrigues, C.I. (author), den Ridder, M.J. (author), Pabst, Martin (author), Gombert, Andreas K. (author), Wahl, S.A. (author)
Both the identity and the amount of a carbon source present in laboratory or industrial cultivation media have major impacts on the growth and physiology of a microbial species. In the case of the yeast Saccharomyces cerevisiae, sucrose is arguably the most important sugar used in industrial biotechnology, whereas glucose is the most common...
journal article 2023
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Gallego Murillo, Joan Sebastián (author), Yağcı, Nurcan (author), Pinho, Eduardo Machado (author), Wahl, S.A. (author), van den Akker, Emile (author), von Lindern, Marieke (author)
Iron, supplemented as iron-loaded transferrin (holotransferrin), is an essential nutrient in mammalian cell cultures, particularly for erythroid cultures. The high cost of human transferrin represents a challenge for large scale production of red blood cells (RBCs) and for cell therapies in general. We evaluated the use of deferiprone, a cell...
journal article 2023
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Olavarria, Karel (author), Sousa, Diana Z. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
Utilizing anaerobic metabolisms for the production of biotechnologically relevant products presents potential advantages, such as increased yields and reduced energy dissipation. However, lower energy dissipation may indicate that certain reactions are operating closer to their thermodynamic equilibrium. While stoichiometric analyses and...
journal article 2023
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Olavarria, Karel (author), Pijman, Yared O. (author), Cabrera, Ricardo (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the...
journal article 2022
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Gallego Murillo, Joan Sebastián (author), Iacono, Giulia (author), van der Wielen, L.A.M. (author), van den Akker, Emile (author), von Lindern, Marieke (author), Wahl, S.A. (author)
Transfusion of donor-derived red blood cells (RBCs) is the most common form of cell therapy. Production of transfusion-ready cultured RBCs (cRBCs) is a promising replacement for the current, fully donor-dependent therapy. A single transfusion unit, however, contains 2 × 10<sup>12</sup> RBC, which requires large scale production. Here, we...
journal article 2022
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Verhagen, K.J.A. (author), Eerden, S. A. (author), Sikkema, B. J. (author), Wahl, S.A. (author)
Exposed to changes in their environment, microorganisms will adapt their phenotype, including metabolism, to ensure survival. To understand the adaptation principles, resource allocation-based approaches were successfully applied to predict an optimal proteome allocation under (quasi) steady-state conditions. Nevertheless, for a general,...
journal article 2022
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McDaniel, Elizabeth A. (author), Wahl, S.A. (author), Ishii, Shun'ichi (author), Pinto, Ameet (author), Ziels, Ryan (author), Nielsen, Per Halkjær (author), McMahon, Katherine D. (author), Williams, Rohan B.H. (author)
Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions – including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful...
review 2021
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Soares Rodrigues, C.I. (author), Wahl, S.A. (author), Gombert, Andreas K. (author)
Present knowledge on the quantitative aerobic physiology of the yeast Saccharomyces cerevisiae during growth on sucrose as sole carbon and energy source is limited to either adapted cells or to the model laboratory strain CEN.PK113-7D. To broaden our understanding of this matter and open novel opportunities for sucrose-based biotechnological...
journal article 2021
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Evers, Bernard (author), Gerding, Albert (author), Boer, Theo (author), Heiner-Fokkema, M. Rebecca (author), Jalving, Mathilde (author), Wahl, S.A. (author), Reijngoud, Dirk Jan (author), Bakker, Barbara M. (author)
13C-isotope tracing is a frequently employed approach to study metabolic pathway activity. When combined with the subsequent quantification of absolute metabolite concentrations, this enables detailed characterization of the metabolome in biological specimens and facilitates computational time-resolved flux quantification. Classically, a 13C...
journal article 2021
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Vasilakou, E. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
Background: Microbial metabolism is highly dependent on the environmental conditions. Especially, the substrate concentration, as well as oxygen availability, determine the metabolic rates. In large-scale bioreactors, microorganisms encounter dynamic conditions in substrate and oxygen availability (mixing limitations), which influence their...
journal article 2020
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Zhang, J. (author), van den Herik, Bas Mees (author), Wahl, S.A. (author)
α-Ketoglutarate (αKG) is a metabolite of the tricarboxylic acid cycle, important for biomass synthesis and a precursor for biotechnological products like 1,4-butanediol. In the eukaryote Saccharomyces cerevisiae αKG is present in different compartments. Compartmentation and (intra-)cellular transport could interfere with heterologous product...
journal article 2020
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Verhagen, K.J.A. (author), van Gulik, W.M. (author), Wahl, S.A. (author)
Redox metabolism plays an essential role in the central metabolic network of all living cells, connecting, but at the same time separating, catabolic and anabolic pathways. Redox metabolism is inherently linked to the excretion of overflow metabolites. Overflow metabolism allows for higher substrate uptake rates, potentially outcompeting...
review 2020
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Olavarria, Karel (author), Almeida Gaspar Carnet, A.E.P. (author), van Renselaar, Joachim (author), Quakkelaar, Caspar (author), Cabrera, Ricardo (author), Gabriel Guedes da Silva, L. (author), Smids, Aron L. (author), Villalobos, Pablo Andres (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
Oxygen supply implies higher production cost and reduction of maximum theoretical yields. Thus, generation of fermentation products is more cost-effective. Aiming to find a key piece for the production of (poly)-3-hydroxybutyrate (PHB) as a fermentation product, here we characterize an acetoacetyl-CoA reductase, isolated from a Candidatus...
journal article 2020
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Olavarria, Karel (author), Quakkelaar, Caspar (author), van Renselaar, Joachim (author), Langerak, D. (author), van Loosdrecht, Mark C.M. (author), Wahl, S.A. (author)
Biosynthesis of poly-3-hydroxybutyrate (PHB) as a fermentation product enables the coupling of growth and product generation. Moreover, the reduction of oxygen supply should reduce operative cost and increase product yield. Generation of PHB as a fermentation product depends on the in vivo activity of an NADH-preferring acetoacetyl-CoA...
journal article 2020
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Couasnon, Anais (author), Eilander, Dirk (author), Muis, Sanne (author), Veldkamp, Ted I.E. (author), Haigh, Ivan D (author), Wahl, Thomas (author), Winsemius, H.C. (author), Ward, Philip J. (author)
The interaction between physical drivers from oceanographic, hydrological, and meteorological processes in coastal areas can result in compound flooding. Compound flood events, like Cyclone Idai and Hurricane Harvey, have revealed the devastating consequences of the co-occurrence of coastal and river floods. A number of studies have recently...
journal article 2020
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Doerr, A. (author), de Reus, Elise (author), van Nies, P.Y.B. (author), van der Haar, Mischa (author), Wei, Katy (author), Kattan, J.M. (author), Wahl, S.A. (author), Danelon, C.J.A. (author)
DNA-guided cell-free protein synthesis using a minimal set of purified components has emerged as a versatile platform in constructive biology. The E. coli-based PURE (protein synthesis using recombinant elements) system offers the basic protein synthesis factory in a prospective minimal cell relying on extant molecules. However, there is an...
journal article 2019
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Zhang, J. (author), Martinez-Gomez, Karla (author), Heinzle, Elmar (author), Wahl, S.A. (author)
Introduction: The switch from quiescence (G0) into G1 and cell cycle progression critically depends on specific nutrients and metabolic capabilities. Conversely, metabolic networks are regulated by enzyme–metabolite interaction and transcriptional regulation that lead to flux modifications to support cell growth. How cells process and...
journal article 2019
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