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Totlani, K. (author), van Tatenhove-Pel, R.J. (author), Kreutzer, M.T. (author), van Gulik, W.M. (author), van Steijn, V. (author)It is common practice in the development of bioprocesses to genetically modify a microorganism and study a large number of resulting mutants in order to select the ones that perform best for use at the industrial scale. At industrial scale, strict nutrient-controlled growth conditions are imposed to control the metabolic activity and growth...review 2023
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Jánoska, A. (author), Buijs, Joran (author), van Gulik, W.M. (author)In large scale fermentors the cultivated cells are exposed to dynamic changes in the nutrient concentrations due to imperfect mixing. Based on the characterization of these nutrient gradients in space and time, a rational scale down design can be obtained. This study focuses on the combined gradients of dissolved sugar and oxygen...journal article 2023
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van Gulik, W.M. (author), Canelas, A (author), Nikerel, I.E. (author), Douma, RD (author), de Jonge, L.P. (author), Heijnen, J.J. (author)Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic...book chapter 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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Jánoska, A. (author), Verheijen, Jelle J. (author), Tang, W. (author), Lee, Queenie (author), Sikkema, Baukje (author), van Gulik, W.M. (author)In large-scale bioreactors, there is often insufficient mixing and as a consequence, cells experience uneven substrate and oxygen levels that influence product formation. In this study, the influence of dissolved oxygen (DO) gradients on the primary and secondary metabolism of a high producing industrial strain of Penicillium chrysogenum was...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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García-Ríos, Estéfani (author), Alonso-del-Real, Javier (author), Lip, K.Y.F. (author), Pinheiro, Tania (author), Teixeira, José (author), van Gulik, W.M. (author), Domingues, Lucília (author), Querol, Amparo (author), Guillamón, José Manuel (author)Understanding of thermal adaptation mechanisms in yeast is crucial to develop better-adapted strains to industrial processes, providing more economical and sustainable products. We have analyzed the transcriptomic responses of three Saccharomyces cerevisiae strains, a commercial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and a...journal article 2022
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Liu, Y. (author), Esen, Osman (author), Pronk, J.T. (author), van Gulik, W.M. (author)This study explores the relation between biomass-specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium-limited aerobic chemostat and retentostat cultures were...journal article 2021
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Totlani, K. (author), Wang, Yen Chieh (author), Bisschops, Maxime (author), de Riese, Thorben (author), Kreutzer, M.T. (author), van Gulik, W.M. (author), van Steijn, V. (author)A key bottleneck in bioprocess development is that state-of-the-art tools used for screening of cells and optimization of cultivation conditions do not represent the conditions enforced at industrial scale. At industrial scale, cell growth is strictly controlled (“fed-batch”) to optimize the metabolites produced by the cells. In contrast,...journal article 2021
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Gelain, L. (author), Geraldo da Cruz Pradella, José (author), Carvalho da Costa, Aline (author), van der Wielen, L.A.M. (author), van Gulik, W.M. (author)Intracellular metabolites were evaluated during the continuous growth of Trichoderma harzianum P49P11 under carbon-limited conditions. Four different conditions in duplicate were investigated (10 and 20 g/L of glucose, 5.26/5.26 g/L of fructose/glucose and 10 g/L of sucrose in the feed). Differences in the values of some specific...journal article 2021
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Pinheiro, Tânia (author), Lip, K.Y.F. (author), García-Ríos, Estéfani (author), Querol, Amparo (author), Teixeira, José (author), van Gulik, W.M. (author), Guillamón, José Manuel (author), Domingues, Lucília (author)Elucidation of temperature tolerance mechanisms in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an...journal article 2020
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Bouman, D. (author), van Gulik, R.J.J. (author), Steffensen, Gorm (author), Pataki, Dávid (author), Boross, Péter (author), Krogstrup, Peter (author), Nygård, Jesper (author), Paaske, Jens (author), Pályi, András (author), Geresdi, A. (author)Serial double quantum dots created in semiconductor nanostructures provide a versatile platform for investigating two-electron spin quantum states, which can be tuned by electrostatic gating and an external magnetic field. In this Rapid Communication, we directly measure the supercurrent reversal between adjacent charge states of an InAs...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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Totlani, K. (author), Hurkmans, Jan Willem (author), van Gulik, W.M. (author), Kreutzer, M.T. (author), van Steijn, V. (author)We developed a microfluidic droplet on-demand (DoD) generator that enables the production of droplets with a volume solely governed by the geometry of the generator for a range of operating conditions. The prime reason to develop this novel type of DoD generator is that its robustness in operation enables scale out and operation under non...journal article 2020
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Lip, K.Y.F. (author), García-Ríos, Estéfani (author), Costa, Carlos E. (author), Guillamón, José Manuel (author), Domingues, Lucília (author), Teixeira, José (author), van Gulik, W.M. (author)A phenotypic screening of 12 industrial yeast strains and the well-studied laboratory strain CEN.PK113-7D at cultivation temperatures between 12 °C and 40 °C revealed significant differences in maximum growth rates and temperature tolerance. From those 12, two strains, one performing best at 12 °C and the other at 40 °C, plus the laboratory...journal article 2020
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Gelain, L. (author), Pabst, Martin (author), da Cruz Pradella, José Geraldo (author), da Costa, Aline Carvalho (author), van der Wielen, L.A.M. (author), van Gulik, W.M. (author)The wild type strain Trichoderma harzianum was able to synthesize enzymes that can catalyse the hydrolysis of p-nitrophenyl-β-D-glucopyranoside (PNPGase) in glucose-limited chemostat cultures. Fructose/glucose and sucrose conditions provided low levels of PNPGase activity. To investigate whether under these conditions other enzymes were...journal article 2020
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Gelain, L. (author), van der Wielen, L.A.M. (author), van Gulik, W.M. (author), da Cruz Pradella, José Geraldo (author), Carvalho da Costa, Aline (author)Cellulase production can be divided into two steps: growth stage; followed by an induction stage. To develop a mathematical model for the optimization of this strategy, two sets of experiments were performed in batch mode for parameter estimation. One set of experiments was performed to evaluate the influence of glycerol regarding cell growth...journal article 2020
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Gelain, L. (author), Kingma, Esther (author), Geraldo da Cruz Pradella, José (author), Carvalho da Costa, Aline (author), van der Wielen, L.A.M. (author), van Gulik, W.M. (author)Carbon-limited chemostat cultures were performed using different carbon sources (glucose, 10 and 20 g/L; sucrose, 10 g/L; fructose/glucose, 5.26/5.26 g/L; carboxymethyl cellulose, 10 g/L; and carboxymethyl cellulose/glucose, 5/5 g/L) to verify the capability of the wild type strain Trichoderma harzianum to produce extracellular enzymes. All...journal article 2020
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Laroche, D. (author), Bouman, D. (author), van Woerkom, D.J. (author), Proutski, A. (author), Murthy, Chaitanya (author), Nayak, Chetan (author), van Gulik, R.J.J. (author), Kouwenhoven, Leo P. (author), Geresdi, A. (author)Quantum computation by non-Abelian Majorana zero modes (MZMs) offers an approach to achieve fault tolerance by encoding quantum information in the non-local charge parity states of semiconductor nanowire networks in the topological superconductor regime. Thus far, experimental studies of MZMs chiefly relied on single electron tunneling...journal article 2019
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Hakkaart, X.D.V. (author), Liu, Y. (author), Hulst, Mandy (author), el Masoudi, Anissa (author), Peuscher, Eveline (author), Pronk, J.T. (author), van Gulik, W.M. (author), Daran-Lapujade, P.A.S. (author)Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic-acid yield and recovery include slow growth, low pH, and high CO<sub>2</sub>. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and...journal article 2019
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