Search Results - "Roubos, Johannes A."

CRISPR/Cpf1 enables fast and simple genome editing of Saccharomyces cerevisiae by Verwaal, René, Buiting‐Wiessenhaan, Nathalie, Dalhuijsen, Sacha, Roubos, Johannes A.

“…Cpf1 represents a novel single RNA‐guided CRISPR/Cas endonuclease system suitable for genome editing with distinct features compared with Cas9. We demonstrate…”
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Multiplex genome editing of microorganisms using CRISPR-Cas by Adiego-Pérez, Belén, Randazzo, Paola, Daran, Jean Marc, Verwaal, René, Roubos, Johannes A, Daran-Lapujade, Pascale, van der Oost, John

“…ABSTRACT Microbial production of chemical compounds often requires highly engineered microbial cell factories. During the last years, CRISPR-Cas nucleases have…”
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Carboxylic acid reductase-dependent biosynthesis of eugenol and related allylphenols by Hanko, Erik K. R, Valdehuesa, Kris Niéo G, Verhagen, Koen J. A, Chromy, Jakub, Stoney, Ruth A, Chua, Jeremy, Yan, Cunyu, Roubos, Johannes A, Schmitz, Joep, Breitling, Rainer

“…Abstract Background (Hydroxy)cinnamyl alcohols and allylphenols, including coniferyl alcohol and eugenol, are naturally occurring aromatic compounds widely…”
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Metabolic enzyme clustering by coiled coils improves the biosynthesis of resveratrol and mevalonate by Fink, Tina, Stevović, Bojana, Verwaal, René, Roubos, Johannes A., Gaber, Rok, Benčina, Mojca, Jerala, Roman, Gradišar, Helena

“…The clustering of biosynthetic enzymes is used in nature to channel reaction products and increase the yield of compounds produced by multiple reaction steps…”
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Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger by van den Berg, Bastiaan A, Reinders, Marcel J T, Hulsman, Marc, Wu, Liang, Pel, Herman J, Roubos, Johannes A, de Ridder, Dick

“…Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing…”
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Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a by Ciurkot, Klaudia, Gorochowski, Thomas E, Roubos, Johannes A, Verwaal, René

“…Abstract CRISPR Cas12a is an RNA-programmable endonuclease particularly suitable for gene regulation. This is due to its preference for T-rich PAMs that allows…”
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Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor by Zhou, Hui, Vonk, Brenda, Roubos, Johannes A, Bovenberg, Roel A L, Voigt, Christopher A

“…Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is…”
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Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate by Gorochowski, Thomas E, Ignatova, Zoya, Bovenberg, Roel A L, Roubos, Johannes A

“…Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables…”
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Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger by Yuan, Xiao-Lian, Roubos, Johannes A, van den Hondel, Cees A. M. J. J, Ram, Arthur F. J

“…The expression of inulinolytic genes in Aspergillus niger is co-regulated and induced by inulin and sucrose. We have identified a positive acting transcription…”
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A Minimal Model of Ribosome Allocation Dynamics Captures Trade-offs in Expression between Endogenous and Synthetic Genes by Gorochowski, Thomas E, Avcilar-Kucukgoze, Irem, Bovenberg, Roel A. L, Roubos, Johannes A, Ignatova, Zoya

“…Cells contain a finite set of resources that must be distributed across many processes to ensure survival. Among them, the largest proportion of cellular…”
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Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast by Young, Eric M., Zhao, Zheng, Gielesen, Bianca E.M., Wu, Liang, Benjamin Gordon, D., Roubos, Johannes A., Voigt, Christopher A.

“…Metabolic engineering requires multiple rounds of strain construction to evaluate alternative pathways and enzyme concentrations. Optimizing multigene pathways…”
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Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability by Wohlgemuth, Sibylle E, Gorochowski, Thomas E, Roubos, Johannes A

“…The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of…”
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Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis by Park, Jong Hyun, Bassalo, Marcelo C., Lin, Geng-Min, Chen, Ye, Doosthosseini, Hamid, Schmitz, Joep, Roubos, Johannes A., Voigt, Christopher A.

“…The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are…”
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CRISPR/Cas12a Multiplex Genome Editing of Saccharomyces cerevisiae and the Creation of Yeast Pixel Art by Ciurkot, Klaudia, Vonk, Brenda, Gorochowski, Thomas E, Roubos, Johannes A, Verwaal, René

“…High efficiency, ease of use and versatility of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system…”
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Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors by Moser, Felix, Broers, Nicolette J, Hartmans, Sybe, Tamsir, Alvin, Kerkman, Richard, Roubos, Johannes A, Bovenberg, Roel, Voigt, Christopher A

“…Synthetic genetic programs promise to enable novel applications in industrial processes. For such applications, the genetic circuits that compose programs will…”
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Novel sequencing technologies to support industrial biotechnology by Costessi, Adalberto, van den Bogert, Bartholomeus, May, Ali, Ver Loren van Themaat, Emiel, Roubos, Johannes A, Kolkman, Marc A B, Butler, Derek, Pirovano, Walter

“…Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed…”
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SPiCE: a web-based tool for sequence-based protein classification and exploration by van den Berg, Bastiaan A, Reinders, Marcel J T, Roubos, Johannes A, de Ridder, Dick

“…Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or…”
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Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli by Gorochowski, Thomas E, van den Berg, Eric, Kerkman, Richard, Roubos, Johannes A, Bovenberg, Roel A. L

“…Synthetic biology has developed numerous parts for the precise control of protein expression. However, relatively little is known about the burden these place…”
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The decarboxylation of the weak-acid preservative, sorbic acid, is encoded by linked genes in Aspergillus spp by Plumridge, Andrew, Melin, Petter, Stratford, Malcolm, Novodvorska, Michaela, Shunburne, Lee, Dyer, Paul S., Roubos, Johannes A., Menke, Hildegard, Stark, Jacques, Stam, Hein, Archer, David B.

“…The ability to resist anti-microbial compounds is of key evolutionary benefit to microorganisms. Aspergillus niger has previously been shown to require the…”
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Protein redesign by learning from data by van den Berg, Bastiaan A., Reinders, Marcel J.T., van der Laan, Jan-Metske, Roubos, Johannes A., de Ridder, Dick

“…Protein redesign methods aim to improve a desired property by carefully selecting mutations in relevant regions guided by protein structure. However, often…”
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