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Filius, M. (author), van Wee, R.G. (author), de Lannoy, C.V. (author), Westerlaken, I. (author), Li, Zeshi (author), Kim, S.H. (author), de Agrela Pinto, C. (author), Wu, Yunfei (author), Boons, Geert-Jan (author), Pabst, Martin (author), de Ridder, Dick (author), Joo, C. (author)Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and...journal article 2024
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Altmann, Friedrich (author), Helm, Johannes (author), Pabst, Martin (author), Stadlmann, Johannes (author)In the beginning was the word. But there were no words for N-glycans, at least, no simple words. Next to chemical formulas, the IUPAC code can be regarded as the best, most reliable and yet immediately comprehensible annotation of oligosaccharide structures of any type from any source. When it comes to N-glycans, the venerable IUPAC code has,...journal article 2024
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Godoy Hernandez, A. (author), Asseri, Amer H. (author), Purugganan, Aiden J. (author), Jiko, Chimari (author), de Ram, C. (author), Lill, Holger (author), Pabst, Martin (author), Mitsuoka, Kaoru (author), Gerle, Christoph (author), Bald, Dirk (author), McMillan, D.G.G. (author)Functional reintegration into lipid environments represents a major challenge for in vitro investigation of integral membrane proteins (IMPs). Here, we report a new approach, termed LMNG Auto-insertion Reintegration (LAiR), for reintegration of IMPs into lipid bilayers within minutes. The resulting proteoliposomes displayed an unprecedented...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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Sorokin, Dimitry Y. (author), Tikhonova, Tamara V. (author), Koch, Hanna (author), van den Berg, E.M. (author), Hinderks, Renske S. (author), Pabst, Martin (author), Kuenen, J.G. (author), van Loosdrecht, Mark C.M. (author), Lücker, Sebastian (author)Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited...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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Keulen, D. (author), van der Hagen, Erik (author), Geldhof, Geoffroy (author), Le Bussy, Olivier (author), Pabst, Martin (author), Ottens, M. (author)An optimal purification process for biopharmaceutical products is important to meet strict safety regulations, and for economic benefits. To find the global optimum, it is desirable to screen the overall design space. Advanced model-based approaches enable to screen a broad range of the design-space, in contrast to traditional statistical or...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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Allaart, M.T. (author), Fox, B.B. (author), Nettersheim, I.H.M.S. (author), Pabst, Martin (author), Sousa, Diana Z. (author), Kleerebezem, R. (author)Hexanoate is a valuable chemical that can be produced by microorganisms that convert short-chain- to medium-chain carboxylic acids through a process called chain elongation. These microorganisms usually produce mixtures of butyrate and hexanoate from ethanol and acetate, but direct conversion of ethanol to hexanoate is theoretically possible....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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Tomas Martinez, S. (author), Zwolsman, Erwin J. (author), Merlier, Franck (author), Pabst, Martin (author), Lin, Y. (author), van Loosdrecht, Mark C.M. (author), Weissbrodt, D.G. (author)Polyphosphate accumulating organisms (PAOs) are responsible for enhanced biological phosphate removal (EBPR) from wastewater, where they grow embedded in a matrix of extracellular polymeric substances (EPS). EPSs comprise a mixture of biopolymers like polysaccharides or (glyco)proteins. Despite previous studies, little is known about the...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), Grouzdev, Denis (author), Schaasberg, P. (author), van Valderen, R.D. (author), van der Zwaan, R. (author), van de Wijgaart, R. (author), Lin, Y. (author), Abbas, B.A. (author), Pronk, M. (author), van Loosdrecht, Mark C.M. (author), Pabst, Martin (author)The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these ...journal article 2023
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Corbera Rubio, F. (author), Laureni, M. (author), Koudijs, N. (author), Müller, S. (author), van Alen, Theo (author), Schoonenberg, Frank (author), Lücker, Sebastian (author), Pabst, Martin (author), van Loosdrecht, Mark C.M. (author), van Halem, D. (author)Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions...journal article 2023
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Hu, Chunyi (author), van Beljouw, S.P.B. (author), Nam, Ki Hyun (author), Schuler, Gabriel (author), Rodríguez Molina, A. (author), van Eijkeren-Haagsma, A.C. (author), Valk, M. (author), Pabst, Martin (author), Brouns, S.J.J. (author)The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo-electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5...journal article 2022
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Cerruti, M. (author), Kim, J.H. (author), Pabst, Martin (author), van Loosdrecht, Mark C.M. (author), Weissbrodt, D.G. (author)Purple bacteria (PPB), anoxygenic photoorganoheterotrophic organisms with a hyper-versatile metabolism and high biomass yields over substrate, are promising candidates for the recovery of nutrient resources from wastewater. Infrared light is a pivotal parameter to control and design PPB-based resource recovery. However, the effects of light...journal article 2022
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Elahinik, A. (author), Haarsma, M.N. (author), Abbas, B.A. (author), Pabst, Martin (author), Xevgenos, Dimitris (author), van Loosdrecht, Mark C.M. (author), Pronk, M. (author)Glycerol is abundantly present in wastewater from industries such as biodiesel production facilities. Glycerol is also a potential carbon source for microbes that are involved in wastewater nutrient removal processes. The conversion of glycerol in biological phosphorus removal of aerobic granular sludge processes has not been explored to date....journal article 2022
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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
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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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Postma, E.D. (author), Else-Hassing, J. (author), Mangkusaputra, Venda (author), Geelhoed, J. (author), de la Torre, P. (author), van den Broek, M.A. (author), Mooiman, C. (author), Pabst, Martin (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)The construction of powerful cell factories requires intensive genetic engineering for the addition of new functionalities and the remodeling of native pathways and processes. The present study demonstrates the feasibility of extensive genome reprogramming using modular, specialized de novo-assembled neochromosomes in yeast. The in vivo...journal article 2022