Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Een uniek project, een unieke samenwerking. De governance van Marker Wadden ontleed : Rapportage MEP Adaptieve Governance Marker Wadden
    IJff, Stéphanie ; Willems, Jannes ; Berg, Niels van den; Nuesink, Nienke ; Kuindersma, Wiebren ; Veraart, Jeroen ; Duijn, Mike ; Ellen, Gerald Jan - \ 2020
    Delft : Deltares - 48
    Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings
    Geshnizjani, Nafiseh ; Snoek, Basten L. ; Willems, Leo A.J. ; Rienstra, Juriaan A. ; Nijveen, Harm ; Hilhorst, Henk W.M. ; Ligterink, Wilco - \ 2020
    Plant, Cell & Environment 43 (2020)8. - ISSN 0140-7791 - p. 1973 - 1988.
    high phosphate - low nitrogen - maternal environment - QTL × E - seed quality - seedling establishment - tomato

    Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (Gmax), germination rate (t50) and uniformity (U8416) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.

    Heritability estimates for 361 blood metabolites across 40 genome-wide association studies
    Hagenbeek, Fiona A. ; Pool, René ; Dongen, Jenny van; Draisma, H.M. ; Jan Hottenga, Jouke ; Willemsen, Gonneke ; Abdellaoui, Abdel ; Fedko, Iryna O. ; Braber, Anouk den; Visser, Pieter Jelle ; Geus, Eco J.C.N. de; Willems van Dijk, Ko ; Verhoeven, Aswin ; Suchiman, H.E. ; Beekman, Marian ; Slagboom, P.E. ; Duijn, Cornelia M. van; Barkey Wolf, J.J.H. ; Cats, D. ; Amin, N. ; Beulens, J.W. ; Bom, J.A. van der; Bomer, N. ; Demirkan, A. ; Hilten, J.A. van; Meessen, J.M.T.A. ; Moed, M.H. ; Fu, J. ; Onderwater, G.L.J. ; Rutters, F. ; So-Osman, C. ; Flier, W.M. van der; Heijden, A.A.W.A. van der; Spek, A. van der; Asselbergs, F.W. ; Boersma, E. ; Elders, P.M. ; Geleijnse, J.M. ; Ikram, M.A. ; Kloppenburg, M. ; Meulenbelt, I. ; Mooijaart, S.P. ; Nelissen, R.G.H.H. ; Netea, M.G. ; Penninx, B.W.J.H. ; Stehouwer, C.D.A. ; Teunissen, C.E. ; Terwindt, G.M. ; Jukema, J.W. ; Reinders, M.J.T. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    The original version of the Supplementary Information associated with this Article included an incorrect Supplementary Data 1 file, in which additional delimiters were included in the first column for a number of rows, resulting in column shifts for some of these rows. The HTML has been updated to include a corrected version of Supplementary Data 1; the original incorrect version of Supplementary Data 1 can be found as Supplementary Information associated with this Correction. In addition, the original version of this Article contained an error in the author affiliations. An affiliation of Abdel Abdellaoui with Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.

    Arabidopsis in the wild—the effect of seasons on seed performance
    Souza Vidigal, Deborah de; He, Hanzi ; Hilhorst, Henk W.M. ; Willems, Leo A.J. ; Bentsink, Leónie - \ 2020
    Plants 9 (2020)5. - ISSN 2223-7747
    Arabidopsis - Environmental effects - Field conditions - Seed dormancy - Seed longevity

    Climate changes play a central role in the adaptive life histories of organisms all over the world. In higher plants, these changes may impact seed performance, both during seed development and after dispersal. To examine the plasticity of seed performance as a response to environmental fluctuations, eight genotypes known to be affected in seed dormancy and longevity were grown in the field in all seasons of two years. Soil and air temperature, day length, precipitation, and sun hours per day were monitored. We show that seed performance depends on the season. Seeds produced by plants grown in the summer, when the days began to shorten and the temperature started to decrease, were smaller with deeper dormancy and lower seed longevity compared to the other seasons when seeds were matured at higher temperature over longer days. The performance of seeds developed in the different seasons was compared to seeds produced in controlled conditions. This revealed that plants grown in a controlled environment produced larger seeds with lower dormancy than those grown in the field. All together the results show that the effect of the environment largely overrules the genetic effects, and especially, differences in seed dormancy caused by the different seasons were larger than the differences between the genotypes.

    Klimaatbestendig Nederland in 2120
    Rooij, Bertram de - \ 2020

    verslag van presentatie van Bertram de Rooij

    COvalent monolayer patterns in Microfluidics by PLasma etching Open Technology-COMPLOT
    Willems, Stan B.J. ; Zegers, Jaccoline ; Bunschoten, Anton ; Wagterveld, Martijn ; Leeuwen, Fijs W.B. Van; Velders, Aldrik H. ; Saggiomo, Vittorio - \ 2020
    The Analyst 145 (2020)5. - ISSN 0003-2654 - p. 1629 - 1635.

    Plasma microcontact patterning (PμCP) and replica molding were combined to make PDMS/glass microfluidic devices with β-cyclodextrin (β-CD) patterns attached covalently on the glass surface inside microchannels. The supramolecular reactivity, reusability and association constant of β-CD with Cy5-Ad2 was tested by analyzing signal-to-noise ratios of patterns vs. spacing with fluorescence microscopy.

    Supramolecular catch and release : Cyclodextrin-functionalized microfluidics for reversible immobilization of (model) bacteria
    Willems, Stan B.J. - \ 2020
    Wageningen University. Promotor(en): A.H. Velders; V. Saggiomo, co-promotor(en): F.W.B. van Leeuwen. - Wageningen : Wageningen University - ISBN 9789463952569 - 162

    The increase in prevalence of pathogenic bacteria coupled provided the motivation for developing and studying platforms for specific on-flow immobilization of bacteria. To approach this goal, we studied the concept of using supramolecular host-guest chemistry for immobilizing model microparticles and bacteria with cyclodextrin functionalized glass surfaces. Fluorescence microscopy was used as the main tool for characterizing surface functionalization and studying surface adhesion interactions.

    The experimental chapters explored important steps for developing platforms to study removal of molecules, microparticles and bacteria:

    • Development of functionalized surfaces patterned with cyclodextrin

    • Incorporation of patterned surfaces within microfluidic devices

    • Immobilization of polystyrene microparticles on cyclodextrin patterned surfaces through host-guest interactions as proof-of-concept and developing a controllable model system

    • Immobilization of bacteria on cyclodextrin patterned surface through including an intermediary targeting molecules

    Results show that the cyclodextrin patterned microfluidic devices are versatile tool for studying immobilization of microparticles, such as polystyrene and bacteria, through supramolecular interactions. The retention of particles was specific and selective for cyclodextrin patterns when functionalized with adamantane moieties.

    Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug–metabolite atlas
    Liu, Jun ; Lahousse, Lies ; Nivard, Michel G. ; Bot, Mariska ; Chen, Lianmin ; Klinken, Jan Bert van; Thesing, Carisha S. ; Beekman, Marian ; Akker, Erik Ben van den; Slieker, Roderick C. ; Waterham, Eveline ; Kallen, Carla J.H. van der; Boer, Irene de; Li-Gao, Ruifang ; Vojinovic, Dina ; Amin, Najaf ; Radjabzadeh, Djawad ; Kraaij, Robert ; Alferink, Louise J.M. ; Murad, Sarwa Darwish ; Uitterlinden, André G. ; Willemsen, Gonneke ; Pool, Rene ; Milaneschi, Yuri ; Heemst, Diana van; Suchiman, H.E. ; Rutters, Femke ; Elders, Petra J.M. ; Beulens, Joline W.J. ; Heijden, Amber A.W.A. van der; Greevenbroek, Marleen M.J. van; Arts, Ilja C.W. ; Onderwater, Gerrit L.J. ; Maagdenberg, Arn M.J.M. van den; Mook-Kanamori, Dennis O. ; Hankemeier, Thomas ; Terwindt, Gisela M. ; Stehouwer, Coen D.A. ; Geleijnse, Johanna M. ; ‘t Hart, Leen M. ; Slagboom, Eline P. ; Dijk, Ko Willems van; Zhernakova, Alexandra ; Fu, Jingyuan ; Penninx, Brenda W.J.H. ; Boomsma, Dorret I. ; Demirkan, Ayşe ; Stricker, Bruno H.C. ; Duijn, Cornelia M. van - \ 2020
    Nature Medicine 26 (2020)1. - ISSN 1078-8956 - p. 110 - 117.

    Progress in high-throughput metabolic profiling provides unprecedented opportunities to obtain insights into the effects of drugs on human metabolism. The Biobanking BioMolecular Research Infrastructure of the Netherlands has constructed an atlas of drug–metabolite associations for 87 commonly prescribed drugs and 150 clinically relevant plasma-based metabolites assessed by proton nuclear magnetic resonance. The atlas includes a meta-analysis of ten cohorts (18,873 persons) and uncovers 1,071 drug–metabolite associations after evaluation of confounders including co-treatment. We show that the effect estimates of statins on metabolites from the cross-sectional study are comparable to those from intervention and genetic observational studies. Further data integration links proton pump inhibitors to circulating metabolites, liver function, hepatic steatosis and the gut microbiome. Our atlas provides a tool for targeted experimental pharmaceutical research and clinical trials to improve drug efficacy, safety and repurposing. We provide a web-based resource for visualization of the atlas (http://bbmri.researchlumc.nl/atlas/).

    Heritability estimates for 361 blood metabolites across 40 genome-wide association studies
    Hagenbeek, Fiona A. ; Pool, René ; Dongen, Jenny van; Draisma, Harmen H.M. ; Hottenga, Jouke Jan ; Willemsen, Gonneke ; Abdellaoui, Abdel ; Fedko, Iryna O. ; Braber, Anouk den; Visser, Pieter Jelle ; Geus, Eco J.C.N. de; Willems van Dijk, Ko ; Verhoeven, Aswin ; Suchiman, H.E. ; Beekman, Marian ; Slagboom, Eline P. ; Duijn, Cornelia M. van; Barkey Wolf, J.J.H. ; Cats, D. ; Amin, N. ; Beulens, J.W. ; Bom, J.A. van der; Bomer, N. ; Demirkan, A. ; Hilten, J.A. van; Meessen, J.M.T.A. ; Moed, M.H. ; Fu, J. ; Onderwater, G.L.J. ; Rutters, F. ; So-Osman, C. ; Flier, W.M. van der; Heijden, A.A.W.A. van der; Spek, A. van der; Asselbergs, F.W. ; Boersma, E. ; Elders, P.M. ; Geleijnse, J.M. ; Ikram, M.A. ; Kloppenburg, M. ; Meulenbelt, I. ; Mooijaart, S.P. ; Nelissen, R.G.H.H. ; Netea, M.G. ; Penninx, B.W.J.H. ; Stehouwer, C.D.A. ; Teunissen, C.E. ; Terwindt, G.M. ; Jukema, J.W. ; Reinders, M.J.T. - \ 2020
    Nature Communications 11 (2020)1. - ISSN 2041-1723

    Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November 2008 and October 2018, and identify >800 class-specific metabolite loci associated with metabolite levels. In a twin-family cohort (N = 5117), these metabolite loci are leveraged to simultaneously estimate total heritability (h2 total), and the proportion of heritability captured by known metabolite loci (h2 Metabolite-hits) for 309 lipids and 52 organic acids. Our study reveals significant differences in h2 Metabolite-hits among different classes of lipids and organic acids. Furthermore, phosphatidylcholines with a high degree of unsaturation have higher h2 Metabolite-hits estimates than phosphatidylcholines with low degrees of unsaturation. This study highlights the importance of common genetic variants for metabolite levels, and elucidates the genetic architecture of metabolite classes.

    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes
    Flood, Pádraic J. ; Theeuwen, Tom P.J.M. ; Schneeberger, Korbinian ; Keizer, Paul ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos A. ; Wijfjes, Raúl ; Calvo-Baltanas, Vanesa ; Becker, Frank F.M. ; Schnabel, Sabine K. ; Willems, Leo A.J. ; Ligterink, Wilco ; Arkel, Jeroen Van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost J.B. ; Eeuwijk, Fred Van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark G.M. ; Wijnker, Erik - \ 2020
    Nature Plants 6 (2020)1. - ISSN 2055-026X - p. 13 - 21.
    Assessment of the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear-derived variation (the nucleotype). Haploid-inducer lines can be used as efficient plasmotype donors to generate new plasmotype–nucleotype combinations (cybrids)1. We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1,859 phenotypes under both stable and fluctuating conditions. We show that natural variation in the plasmotype results in both additive and epistatic effects across all phenotypic categories. Plasmotypes that induce more additive phenotypic changes also cause more epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average, epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multi-level nucleotype–plasmotype–environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation that is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a rapid and precise method for assessment of the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype–plasmotype combinations to both improve our understanding of natural variation in these combinations and identify favourable combinations to enhance plant performance.
    Virtual internships in blended environments to prepare preservice teachers for the professional teaching context
    Theelen, H. ; Willems, M.C. ; Beemt, A. van den; Conijn, R. ; Brok, P. den - \ 2020
    British Journal of Educational Technology 51 (2020)1. - ISSN 0007-1013 - p. 194 - 210.
    This study investigated to what extent virtual internships in teacher education were able to reduce Preservice Teachers’ (PSTs) professional anxiety. Simultaneously, this study investigated how virtual internships in blended learning environments were evaluated by PSTs in terms of technological, social and educational affordances. PSTs followed virtual internships during two different Educational Pedagogy Master’s courses (27 and 16 participants) in a teacher education programme. A mixed methods design was employed, consisting of pre‐ and post‐test questionnaires, a focus group interview and individual interviews. A significant decrease was found in PSTs’ professional anxiety after having followed Virtual Internship 2. PSTs reported they obtained a more realistic image of teaching and felt better prepared for teaching in practice. Furthermore, regarding technological affordances, system usability was considered between acceptable and good. Concerning social affordances, PSTs appreciated collaboration within the virtual internships. As an educational affordance, it appeared that learning from videos with authentic classroom events is a good preparation for the professional teaching context. According to the PSTs, the scenarios within virtual internships could be improved in terms of authenticity and personalisation by offering more details and background information. The results of this study imply that virtual internships can be useful assets for teacher education
    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - RNA Sequencing
    Flood, Padraic ; Theeuwen, Tom ; Schneeberger, Korbinian ; Keizer, Paul ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos ; Wijfjes, Raul ; Calvo Baltanas, Vanesa ; Becker, Frank ; Schnabel, Sabine ; Willems, Leo ; Ligterink, Wilco ; Arkel, Jeroen van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost ; Eeuwijk, Fred van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark ; Wijnker, Erik - \ 2019
    Wageningen University
    PRJEB35324 - ERP118362 - Arabidopsis thaliana - RNA Sequencing - Cybrids
    Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype x Plasmotype x Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype-plasmotype interactions and identify favourable combinations to improve plant performance.
    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes
    Theeuwen, Tom ; Flood, Padraic ; Schneeberger, Korbinian ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos ; Wijfjes, Raul ; Calvo Baltanas, Vanesa ; Becker, Frank ; Schnabel, Sabine ; Willems, Leo ; Ligterink, Wilco ; Arkel, Jeroen van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost ; Eeuwijk, Fred van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark ; Wijnker, Erik - \ 2019
    Wageningen University & Research
    Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype x Plasmotype x Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype-plasmotype interactions and identify favourable combinations to improve plant performance.
    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - Whole Genome Sequencing
    Flood, Padraic ; Theeuwen, Tom ; Schneeberger, Korbinian ; Keizer, Paul ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos ; Wijfjes, Raul ; Calvo Baltanas, Vanesa ; Becker, Frank ; Schnabel, Sabine ; Willems, Leo ; Ligterink, Wilco ; Arkel, Jeroen van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost ; Eeuwijk, Fred van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark ; Wijnker, Erik - \ 2019
    Wageningen University
    PRJEB29654 - ERP111970 - Arabidopsis thaliana - Whole Genome Sequencing - Cybrids
    Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype x Plasmotype x Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype-plasmotype interactions and identify favourable combinations to improve plant performance.
    Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency
    Mierlo, Guido van; Dirks, René A.M. ; Clerck, Laura De; Brinkman, Arie B. ; Huth, Michelle ; Kloet, Susan L. ; Saksouk, Nehmé ; Kroeze, Leonie I. ; Willems, Sander ; Farlik, Matthias ; Bock, Christoph ; Jansen, Joop H. ; Deforce, Dieter ; Vermeulen, Michiel ; Déjardin, Jérôme ; Dhaenens, Maarten ; Marks, Hendrik - \ 2019
    Cell Stem Cell 24 (2019)1. - ISSN 1934-5909 - p. 123 - 137.e8.
    chromatin profiling - embryonic stem cells - epigenetics - ground-state pluripotency - H3K27me3 - histone modifications

    Marks and colleagues use integrative mass spectrometry to profile post-translational histone modifications and the chromatin-associated proteome in ground-state pluripotency. This reveals H3K27me3 and PRC2 as widespread hallmarks on euchromatin and heterochromatin. They show that ubiquitous chromatin-associated PRC2 protects the epigenome from priming, in particular from gaining DNA methylation.

    Bianca strijdt tegen vage menukaarten: ‘Zuurgraad? Dat klinkt niet lekker’
    Wamelink, Wieger - \ 2019
    Is less readable liked better? The case of font readability in poetry appreciation
    Gao, Xin ; Dera, Jeroen ; Nijhof, Annabel D. ; Willems, Roel M. - \ 2019
    PLoS ONE 14 (2019)12. - ISSN 1932-6203

    Previous research shows conflicting findings for the effect of font readability on comprehension and memory for language. It has been found that—perhaps counterintuitively–a hard to read font can be beneficial for language comprehension, especially for difficult language. Here we test how font readability influences the subjective experience of poetry reading. In three experiments we tested the influence of poem difficulty and font readability on the subjective experience of poems. We specifically predicted that font readability would have opposite effects on the subjective experience of easy versus difficult poems. Participants read poems which could be more or less difficult in terms of conceptual or structural aspects, and which were presented in a font that was either easy or more difficult to read. Participants read existing poems and subsequently rated their subjective experience (measured through four dependent variables: overall liking, perceived flow of the poem, perceived topic clarity, and perceived structure). In line with previous literature we observed a Poem Difficulty x Font Readability interaction effect for subjective measures of poetry reading. We found that participants rated easy poems as nicer when presented in an easy to read font, as compared to when presented in a hard to read font. Despite the presence of the interaction effect, we did not observe the predicted opposite effect for more difficult poems. We conclude that font readability can influence reading of easy and more difficult poems differentially, with strongest effects for easy poems.

    Moderne Ark van Noach bevat alle zaden ter wereld
    Hintum, Theo van - \ 2019
    On-Flow Immobilization of Polystyrene Microspheres on β-Cyclodextrin-Patterned Silica Surfaces through Supramolecular Host-Guest Interactions
    Willems, Stan B.J. ; Bunschoten, Anton ; Wagterveld, R.M. ; Leeuwen, Fijs W.B. Van; Velders, Aldrik H. - \ 2019
    ACS Applied Materials and Interfaces 11 (2019)39. - ISSN 1944-8244 - p. 36221 - 36231.
    flow cell - microcontact printing - microparticles - supramolecular chemistry - water purification

    Species-specific isolation of microsized entities such as microplastics and resistant bacteria from waste streams is becoming a growing environmental challenge. By studying the on-flow immobilization of micron-sized polystyrene particles onto functionalized silica surfaces, we ascertain if supramolecular host-guest chemistry in aqueous solutions can provide an alternative technology for water purification. Polystyrene particles were modified with different degrees of adamantane (guest) molecules, and silica surfaces were patterned with β-cyclodextrin (β-CD, host) through microcontact printing (μCP). The latter was exposed to solutions of these particles flowing at different speeds, allowing us to study the effect of flow rate and multivalency on particle binding to the surface. The obtained binding profile was correlated with Comsol simulations. We also observed that particle binding is directly aligned with particle's ability to form host-guest interactions with the β-CD-patterned surface, as particle binding to the functionalized glass surface increased with higher adamantane load on the polystyrene particle surface. Because of the noncovalent character of these interactions, immobilization is reversible and modified β-CD surfaces can be recycled, which provides a positive outlook for their incorporation in water purification systems.

    Nature of Amorphous Hydrophilic Block Affects Self-Assembly of an Artificial Viral Coat Polypeptide
    Willems, Lione ; Westerveld, Larissa Van; Roberts, Stefan ; Weitzhandler, Isaac ; Calcines Cruz, Carlos ; Hernandez-Garcia, Armando ; Chilkoti, Ashutosh ; Mastrobattista, Enrico ; Oost, John Van Der; Vries, Renko De - \ 2019
    Biomacromolecules 20 (2019)10. - ISSN 1525-7797 - p. 3641 - 3647.

    Consensus motifs for sequences of both crystallizable and amorphous blocks in silks and natural structural analogues of silks vary widely. To design novel silklike polypeptides, an important question is therefore how the nature of either the crystallizable or the amorphous block affects the self-assembly and resulting physical properties of silklike polypeptides. We address herein the influence of the amorphous block on the self-assembly of a silklike polypeptide that was previously designed to encapsulate single DNA molecules into rod-shaped viruslike particles. The polypeptide has a triblock architecture, with a long N-terminal amorphous block, a crystallizable midblock, and a C-terminal DNA-binding block. We compare the self-assembly behavior of a triblock with a very hydrophilic collagen-like amorphous block (GXaaYaa)132 to that of a triblock with a less hydrophilic elastin-like amorphous block (GSGVP)80. The amorphous blocks have similar lengths and both adopt a random coil structure in solution. Nevertheless, atomic force microscopy revealed significant differences in the self-assembly behavior of the triblocks. If collagen-like amorphous blocks are used, there is a clear distinction between very short polypeptide-only fibrils and much longer fibrils with encapsulated DNA. If elastin-like amorphous blocks are used, DNA is still encapsulated, but the polypeptide-only fibrils are now much longer and their size distribution partially overlaps with that of the encapsulated DNA fibrils. We attribute the difference to the more hydrophilic nature of the collagen-like amorphous block, which more strongly opposes the growth of polypeptide-only fibrils than the elastin-like amorphous blocks. Our work illustrates that differences in the chemical nature of amorphous blocks can strongly influence the self-assembly and hence the functionality of engineered silklike polypeptides.

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