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de Jong, S.I. (author)Alkaliphiles thrive in environments with a pH of 8.5 or above, while maintaining an internal pH closer to neutral. Thus, alkaliphilic microorganisms have a proton gradient inverted with respect to the normal orientation. Intuitively, this would nullify the potential to generate energy via respiration with regularly oriented respiratory chains...doctoral thesis 2024
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Zhang, M. (author)A remarkable accomplishment of human beings in recent centuries is the extension of their average lifespan, for example by improved living conditions. A downside of this achievement is that aging-related diseases, such as Alzheimer’s disease (AD), have risen, and as a consequence are impacting the lives of an increasing fraction of individuals....doctoral thesis 2023
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den Ridder, M.J. (author)Mass spectrometry-based cellular proteomics has taken a prominent role in many fields of research, including life sciences, biotechnology and microbial ecology. Still, advanced mass spectrometry-based proteomics methods are not routinely applied to microbes. The cell factory and model organism Saccharomyces cerevisiae, for example, is very well...doctoral thesis 2023
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de Bakker, Marie (author), Petersen, Teun B. (author), Rueten-Budde, Anja J. (author), Akkerhuis, K. Martijn (author), Umans, Victor A. (author), Brugts, Jasper J. (author), Germans, Tjeerd (author), Reinders, M.J.T. (author), Katsikis, Peter D. (author)Aims Risk assessment tools are needed for timely identification of patients with heart failure (HF) with reduced ejection fraction (HFrEF) who are at high risk of adverse events. In this study, we aim to derive a small set out of 4210 repeatedly measured proteins, which, along with clinical characteristics and established biomarkers, carry...journal article 2023
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Disela, R.C. (author), Bussy, Olivier Le (author), Geldhof, Geoffroy (author), Pabst, Martin (author), Ottens, M. (author)Mass-spectrometry-based proteomics is increasingly employed to monitor purification processes or to detect critical host cell proteins in the final drug substance. This approach is inherently unbiased and can be used to identify individual host cell proteins without prior knowledge. In process development for the purification of new...journal article 2023
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den Ridder, M.J. (author), van den Brandeler, Wiebeke (author), Altiner, Meryem (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)The yeast Saccharomyces cerevisiae is a widely-used eukaryotic model organism and a promising cell factory for industry. However, despite decades of research, the regulation of its metabolism is not yet fully understood, and its complexity represents a major challenge for engineering and optimizing biosynthetic routes. Recent studies have...journal article 2023
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de Jong, S.I. (author), Sorokin, Dimitry Y. (author), van Loosdrecht, Mark C.M. (author), Pabst, Martin (author), McMillan, D.G.G. (author)Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound...journal article 2023
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Sharman, Kavya (author), Patterson, Nathan Heath (author), Weiss, Andy (author), Neumann, Elizabeth K. (author), Guiberson, Emma R. (author), Ryan, Daniel J. (author), Gutierrez, Danielle B. (author), Spraggins, Jeffrey M. (author), Van de Plas, Raf (author), Skaar, Eric P. (author), Caprioli, Richard M. (author)Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate...journal article 2023
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Elahinik, A. (author), Li, L.H (author), Pabst, Martin (author), Abbas, B.A. (author), Xevgenos, Dimitris (author), van Loosdrecht, Mark C.M. (author), Pronk, M. (author)Enhanced biological phosphate removal and aerobic sludge granulation are commonly studied with fatty acids as substrate. Fermentative substrates such as glucose have received limited attention. In this work, glucose conversion by aerobic granular sludge and its impact on phosphate removal was studied. Long-term stable phosphate removal and...journal article 2023
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Kleikamp, H.B.C. (author)The large unexplored space of microbial biodiversity forms a well of untapped potential of enzymes and bioactive compounds. Genomic methods have made significant improvements over the past decades in their analysis of microbial communities. However, several aspects of nature can’t be described by a genome alone, such as expressed functions in...doctoral thesis 2022
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Kouba, V. (author), Bachmannová, Ch (author), Podzimek, T. (author), Lipovová, P. (author), van Loosdrecht, Mark C.M. (author)The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies...review 2022
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Bourgonje, Arno R. (author), Hu, Shixian (author), Spekhorst, Lieke M. (author), Zhernakova, Daria V. (author), Vila, Arnau Vich (author), Li, Yanni (author), Charrout, M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Background and Aims: Protein profiling in patients with inflammatory bowel diseases [IBD] for diagnostic and therapeutic purposes is underexplored. This study analysed the association between phenotype, genotype, and the plasma proteome in IBD. Methods: A total of 92 inflammation-related proteins were quantified in plasma of 1028 patients...journal article 2022
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Su, Pin Rui (author), You, L. (author), Beerens, Cecile (author), Bezstarosti, Karel (author), Demmers, J.A.A. (author), Pabst, Martin (author), Kanaar, R. (author), Hsu, Cheng Chih (author), Chien, M.P. (author)Single-cell proteomics has the potential to decipher tumor heterogeneity, and a method like single-cell proteomics by mass spectrometry (SCoPE-MS) allows profiling several tens of single cells for >1,000 proteins per cell. This method, however, cannot link the proteome of individual cells with phenotypes of interest. Here, we developed a...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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den Ridder, M.J. (author), Knibbe, E. (author), van den Brandeler, Wiebeke (author), Daran-Lapujade, P.A.S. (author), Pabst, Martin (author)The importance of obtaining comprehensive and accurate information from cellular proteomics experiments asks for a systematic investigation of sample preparation protocols. In particular when working with unicellular organisms with strong cell walls, such as found in the model organism and cell factory Saccharomyces cerevisiae. Here, we...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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Soares Rodrigues, C.I. (author)In recent decades, there has been an increase demand for renewable sources of energy and chemicals in replacement of their fossil-based counterparts to tackle the economic, social, and environmental issues associated with the processing and use of petrochemicals by humanity. Sucrose has proven to be a suitable alternative feedstock to substitute...doctoral thesis 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
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Lawson, Christopher E. (author), Mundinger, Aniela B. (author), Koch, Hanna (author), Jacobson, Tyler B. (author), Weathersby, Coty A. (author), Jetten, Mike S.M. (author), Pabst, Martin (author), Amador-Noguez, Daniel (author), Noguera, Daniel R. (author)Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple...journal article 2021
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Noga, M.J. (author), Büke, F. (author), van den Broek, N.J.F. (author), Imholz, N.C.E. (author), Scherer, N.M.D. (author), Yang, Y.H.F. (author), Bokinsky, G.E. (author)Every cell must produce enough membrane to contain itself. However, the mechanisms by which the rate of membrane synthesis is coupled with the rate of cell growth remain unresolved. By comparing substrate and enzyme concentrations of the fatty acid and phospholipid synthesis pathways of Escherichia coli across a 3-fold range of carbon-limited...journal article 2020
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