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How can something empty be so full: Virus-like particles as next generation vaccines

Kuijpers, L.C. (author)

Vaccination is the most effective strategy in humanity’s fight against viruses. The concept of vaccination was first proposed by dr. Edward Jenner in the 18th Century, and its efficacy has been proven over time, providing unparalleled protection against viral infections. Large-scale vaccination campaigns have been successful in eradicating...

doctoral thesis 2023

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Automated cell counting for Trypan blue-stained cell cultures using machine learning

Kuijpers, L.C. (author), van Veen, E.N.W. (author), Van der Pol, Leo (author), Dekker, N.H. (author)

Cell counting is a vital practice in the maintenance and manipulation of cell cultures. It is a crucial aspect of assessing cell viability and determining proliferation rates, which are integral to maintaining the health and functionality of a culture. Additionally, it is critical for establishing the time of infection in bioreactors and...

journal article 2023

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Beyond Saccharomyces pastorianus for modern lager brews: Exploring non-cerevisiae Saccharomyces hybrids with heterotic maltotriose consumption and novel aroma profile

Gyurchev, Nikola Y. (author), Coral-Medina, Ángela (author), Weening, S.M. (author), Almayouf, Salwa (author), Kuijpers, Niels G.A. (author), Nevoigt, Elke (author), Louis, Edward J. (author)

Non-domesticated, wild Saccharomyces yeasts have promising characteristics for beer diversification, particularly when used in the generation of de novo interspecific hybrids. A major motivation for the current work was the question whether attractive novel Saccharomyces interspecific hybrids can be created for the production of exotic lager...

journal article 2022

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Characterizing single-molecule dynamics of viral RNA-dependent RNA polymerases with multiplexed magnetic tweezers

Kuijpers, L.C. (author), van Laar, T. (author), Janissen, R. (author), Dekker, N.H. (author)

Multiplexed single-molecule magnetic tweezers (MT) have recently been employed to probe the RNA synthesis dynamics of RNA-dependent RNA polymerases (RdRp). Here, we present a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases with MT. We describe the preparation of a dsRNA construct for probing...

journal article 2022

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Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses

Janissen, R. (author), Woodman, Andrew (author), Shengjuler, Djoshkun (author), Vallet, Thomas (author), Lee, Kuo Ming (author), Kuijpers, L.C. (author), Moustafa, Ibrahim M. (author), Fitzgerald, Fiona (author), Dekker, N.H. (author)

Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics...

journal article 2021

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The Trust Game: The influence of Trust on Collaboration in the light of Technological Innovations

Kuijpers, A.G.J. (author), Lukosch, Heide (author), Verbraeck, A. (author)

Adopting innovations is key for organizations to compete in a complex system, such as the transportation system. In a complex system where social (e.g. organizations) and technical (e.g. information systems) interact with each other, collaboration can be challenging. One of the barriers identified that hampers collaboration is trust. To...

conference paper 2021

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In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation

Brouwers, N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Weening, S.M. (author), Elink Schuurman, Tom D. (author), Kuijpers, Niels G.A. (author), Pronk, J.T. (author), Daran, J.G. (author)

Saccharomyces eubayanus is the non-S. cerevisiae parent of the lager-brewing hybrid S. pastorianus. In contrast to most S. cerevisiae and Frohberg-type S. pastorianus strains, S. eubayanus cannot utilize the α-tri-glucoside maltotriose, a major carbohydrate in brewer's wort. In Saccharomyces yeasts, utilization of maltotriose is encoded by...

journal article 2019

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Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Salazar, A.N. (author), Gorter de Vries, A.R. (author), van den Broek, M.A. (author), Brouwers, N. (author), de la Torre, P. (author), Kuijpers, N.G.A. (author), Daran, J.G. (author), Abeel, T.E.P.M.F. (author)

Background: The lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2...

journal article 2019

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Cell Boundary Confinement Sets the Size and Position of the E. coli Chromosome

Wu, Fabai (author), Swain, Pinaki (author), Kuijpers, L.C. (author), Zheng, X.Z. (author), Felter, K.M. (author), Guurink, M. (author), Solari, Jacopo (author), Jun, Suckjoon (author), Dekker, C. (author)

Although the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non...

journal article 2019

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Phenotype-independent isolation of interspecies Saccharomyces hybrids by dual-dye fluorescent staining and fluorescence-activated cell sorting

Gorter de Vries, A.R. (author), Koster, C.C. (author), Weening, S.M. (author), Luttik, M.A.H. (author), Kuijpers, N.G.A. (author), Geertman, Jan Maarten A. (author), Pronk, J.T. (author), Daran, J.G. (author)

Interspecies hybrids of Saccharomyces species are found in a variety of industrial environments and often outperform their parental strains in industrial fermentation processes. Interspecies hybridization is therefore increasingly considered as an approach for improvement and diversification of yeast strains for industrial application....

journal article 2019

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Exploring a Mixed Method Approach: Simulation Games and Q Methodology

Kuijpers, A.G.J. (author), Lukosch, Heide (author), Verbraeck, A. (author)

In this paper we explore the possibilities to combine two research methods we regard as being very useful when interacting with stakeholders in complex systems. We discuss a mixed research methods approach, based on the Q methodology and a simulation game. In a game design process, translating the real or reference system into the game design is...

conference paper 2019

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Agricultural Platforms

Muñoz Sanz, V. (author), Kuijpers, Marten (author), Jaoude, Grace Abou (author)

journal article 2018

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Amino acid profiling from fingerprints, a novel methodology using UPLC-MS

Van Helmond, Ward (author), Kuijpers, Chris Jan (author), Van Diejen, Elise (author), Spiering, Jincey (author), Maagdelijn, Brent (author), de Puit, M. (author)

Fingermark evidence is extensively used in criminal investigations. Hence, there have been many investigations into the chemical compounds present in fingerprint deposits. In this technical note we describe the analysis of non-derivatised amino acid profiles obtained from fingerprints. We used UPLC with an amide stationary phase and...

journal article 2017

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Evolutionary engineering in chemostat cultures for improved maltotriose fermentation kinetics in saccharomyces pastorianus lager brewing yeast

Brickwedde, A. (author), van den Broek, M.A. (author), Geertman, Jan Maarten A. (author), Magalhães, Frederico (author), Kuijpers, Niels G.A. (author), Gibson, Brian (author), Pronk, J.T. (author), Daran, J.G. (author)

The lager brewing yeast Saccharomyces pastorianus, an interspecies hybrid of S. eubayanus and S. cerevisiae, ferments maltotriose, maltose, sucrose, glucose and fructose in wort to ethanol and carbon dioxide. Complete and timely conversion ("attenuation") of maltotriose by industrial S. pastorianus strains is a key requirement for process...

journal article 2017

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Quantitative comparisons of the color of CuAs, CuSn, CuNi, and CuSb alloys

Mödlinger, Marianne (author), Kuijpers, M.H.G. (author), Braekmans, D. (author), Berger, Daniel (author)

The colors of copper alloys are of particular interest in archaeology and can be characterized quantitatively and systematically. The CIELAB color system can determine different color parameters such as a* b* and L* by means of a spectrophotometer that describes the surface color. Additional information such as C* and h values can be...

journal article 2017

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Engineering synthetic glycolytic pathways in Saccharomyes cerevisiae

Kuijpers, N.G.A. (author)

In the past few decades, concerns on climate change have contributed to the development of biotechnological alternatives for petrochemical processes. In order to make these processes economically competitive, there has been an intensive search for improved, more efficient production organisms. In the past decade, genetic engineering of...

doctoral thesis 2016

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A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism

Solis-Escalante, D. (author), Kuijpers, N.G.A. (author), Barrajon-Simancas, N. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P. (author)

As a result of ancestral whole-genome and small-scale duplication events, the genomes of Saccharomyces cerevisiae and many eukaryotes still contain a substantial fraction of duplicated genes. In all investigated organisms, metabolic pathways, and more particularly glycolysis, are specifically enriched for functionally redundant paralogs. In...

journal article 2015

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CRISPR/Cas9: A molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

Mans, R. (author), Van Rossum, H.M. (author), Wijsman, M. (author), Backx, A. (author), Kuijpers, N.G.A. (author), van den Broek, M. (author), Daran-Lapujade, P.A.S. (author), Pronk, J.T. (author), Van Maris, A.J.A. (author), Daran, J.G. (author)

A variety of techniques for strain engineering in Saccharomyces cerevisiae have recently been developed. However, especially when multiple genetic manipulations are required, strain construction is still a time-consuming process. This study describes new CRISPR/Cas9-based approaches for easy, fast strain construction in yeast and explores their...

journal article 2015

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One-step assembly and targeted integration of multigene constructs assisted by the I-SceI meganuclease in Saccharomyces cerevisiae

Kuijpers, N.G.A. (author), Chroumpi, S. (author), Vos, T. (author), Solis-Escalante, D. (author), Bosman, D. (author), Pronk, J.T. (author), Daran, J.G. (author), Daran-Lapujade, P.A.S. (author)

In vivo assembly of overlapping fragments by homologous recombination in Saccharomyces cerevisiae is a powerful method to engineer large DNA constructs. Whereas most in vivo assembly methods reported to date result in circular vectors, stable integrated constructs are often preferred for metabolic engineering as they are required for large-scale...

journal article 2013

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A versatile, efficient strategy for assembly of multi-fragment expression vectors in Saccharomyces cerevisiae using 60 bp synthetic recombination sequences

Kuijpers, N.G. (author), Solis-Escalante, D. (author), Bosman, L. (author), Van den Broek, M. (author), Pronk, J.T. (author), Daran, J.M. (author), Daran-Lapujade, P.A.S. (author)

Background: In vivo recombination of overlapping DNA fragments for assembly of large DNA constructs in the yeast Saccharomyces cerevisiae holds great potential for pathway engineering on a small laboratory scale as well as for automated high-throughput strain construction. However, the current in vivo assembly methods are not consistent with...

journal article 2013