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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    3. De verscheidenheid van bijen en andere insecten : Biodiversiteit.
    Scheer, Henk van der; Blacquiere, T. - \ 2020
    Bijenhouden 2020 (2020)4. - ISSN 1877-9786 - p. 7 - 9.
    Dit keer is de verscheidenheid van insecten, in het bijzonder van bijen, het onderwerp. Bijen verschenen ongeveer 100 miljoen jaar geleden op aarde toen tijdens het Krijt de eerste planten kleurrijke en zoetgeurende bloemen ontwikkelden. De westerse honingbijen verschenen pas 6-8 miljoen jaar geleden als afsplitsing van de meest verwante soort Apis cerana.
    Effecten van klimaatverandering : Biodiversiteit
    Scheer, Henk van der; Blacquiere, T. - \ 2020
    Bijenhouden 14 (2020)5. - ISSN 1877-9786 - p. 7 - 9.
    In het vorige nummer van Bijenhouden vermeldden we al dat de mate van verscheidenheid van soorten nauw samenhangt met het milieu en het klimaat. Dit keer gaat het voornamelijk over de effecten van het klimaat op de biodiversiteit.
    Sensors and sensibility : Tailoring the mechano-responsivity of macromolecules & polymer materials
    Scheer, Pieter Cornelis van der - \ 2020
    Wageningen University. Promotor(en): J.H.B. Sprakel. - Wageningen : Wageningen University - ISBN 9789463953962 - 206

    This thesis describes our explorations in the development of new molecular tools to probe complex soft material systems at the nanoscale. In large part, our efforts have been dedicated to conjugated polymer-based molecular sensors for applications in complex fluids. We have contributed both to developing new chemical strategies for incorporating new function in these macromolecular sensors, but also to develop a deeper understanding of how they work and what their intrinsic limitations are.

    In Chapters 2, 3, 5 we explore new ways to introduce mechanoresponsive moieties into the backbone of semiconducting sensor polymers. In Chapter 2 we introduce a spiropyran moiety into a polyfluorene backbone. Spiropyran functions as a molecular switch whose two states exhibit unique photochromic properties. The molecular switch can be activated by a variety of triggers including but not limited to mechanical-, pH-, light- and temperature-stimuli, and is thermally reversible in the small molecule state. Incorporated into the extended π-conjugated system of a semiconducting polymer backbone, activation of these molecular switches results in spectroscopic shifts of the complete semi-conducting system and a loss of the thermal reversibility. We explore the influence of different chain architectures of spiropyran-co-fluorene polymers and the consequences of expanding the conjugation length of the spiropyran monomer on its switching properties.

    In Chapter 5 we continue along this concept, by introducing a different type of molecular switch into polyfluorene backbones. Here we focus our attention to anthracene monomers, which remain susceptible to modification via a Diels-Alder reaction also post-polymerisation. The Diels-Alder adduct occurs anti-parallel on the central benzene ring of the anthracene causing splitting of conjugation into two isolated systems, thereby interrupting the flow of electrons along the semiconducting polymer backbone and straining the macromolecular conformation. Retro-Diels-Alder reactions, which restore the extended π-conjugation is shown to be achievable both thermally and mechanically. The Diels-Alder adduct of these poly(fluorene-co-anthracene) polymers results in polymers with switchable conjugation. Moreover, we show how tuning of the composition of the polymers enables the tuning of the pre-strain existing on the Diels-Alder adduct and thereby tailoring of the easy of activation and the rate at which this occurs.

    In Chapter 3 we investigate a different route to create mechano-responsive semiconducting polymers, by the introduction of a molecular rotor into the backbone of a semiconducting chain. These small molecule molecular rotors have been widely applied as rigidochromic probes, e.g. as free volume probes in a variety of complex experimental systems. We incorporate the rotating phenyl group of a BODIPY rotor into the π-extended system of a polyfluorene polymer. We show that the energetic separation of the rotating moiety and the BODIPY core remains proficient to retain its rigidochromic properties. Furthermore, the spectral separation between the non-responsive blue backbone emission and the responsive green bodipy emission creates an internal fluorescence emission standard. The energy transfer from the donor backbone to the acceptor rotor ensures this can be achieved using a single channel blue excitation source. This allows for the polymer to be used as a ratiometric free volume sensor in fluorescence imaging while maintaining high spectral and temporal resolution.

    Previous work from our group showed how acceptor-doped conjugated polymers are very well suited for use as molecular mechanosensors. Yet various effects remained poorly explored. In Chapter 4, we investigate chain-length effects on the energy transfer within acceptor-doped conjugated polymer sensors. We perform an exhaustive fractionation of a polymer batch into different fractions of higher monodispersity and different chain lengths. Using a combination of extensive spectroscopic study and Monte Carlo simulations, we show that the interplay between both chain-length and acceptor doping degree play a fundamental role in the usability of an acceptor based conjugated polymer as a strain sensor. We attribute this to a probabilistic process which occurs during the growth of the polymer chain in its synthesis. Although the law of large numbers averages these effects out for a homogeneous batch of sufficiently long polymers this is often ignored for shorter polymers. These results provide fundamental insights into the function of macromolecular strain sensors and guidelines how their use can be improved.

    In addition to main theme of this thesis, as summarized above, a side-project on the assembly and phase behavior of soft colloids resulted in two published chapters. Both chapters aimed to understand how the details of the softness of small colloidal particles changes their properties in large ensembles in dense suspensions. In Chapter 6 we use experiments and theory to explain how the softness of particles changes the apparent way in which the liquid suspension turns solid and how these apparent changes vanish when correcting for the size changes inherent to soft particles. This resolves an open issue in the field of colloidal glasses. In Chapter 7 we continue this exploration by studying how softness, and in particular details on the shape of the soft potential, alters the formation of ordered phases. We show how small changes in the interaction potential can sort large changes in the crystal structures formed. These in-silico results provide guides to the preparation of non-close-packed and non-hexagonal crystal symmetries using colloidal particles as the building blocks.

    2. De natuur heeft een geweldige belevingswaarde
    Scheer, Henk van der; Blacquiere, T. - \ 2020
    Bijenhouden 14 (2020)3. - ISSN 1877-9786 - p. 7 - 9.
    Gebruik de juiste argumenten als je biodiversiteit wilt behouden. Het gaat niet alleen om aantallen soorten behouden of opkrikken, maar vooral om kwaliteit.
    Transcriptome sequencing supports a conservation of macrophage polarization in fish
    Wentzel, Annelieke S. ; Petit, Jules ; Veen, Wouter G. van; Rosenbek Fink, Inge ; Scheer, Marleen H. ; Piazzon, Carla M. ; Forlenza, Maria ; Spaink, Herman P. ; Wiegertjes, Geert F. - \ 2020
    Scientific Reports 10 (2020). - ISSN 2045-2322

    Mammalian macrophages can adopt polarization states that, depending on the exact stimuli present in their extracellular environment, can lead to very different functions. Although these different polarization states have been shown primarily for macrophages of humans and mice, it is likely that polarized macrophages with corresponding phenotypes exist across mammals. Evidence of functional conservation in macrophages from teleost fish suggests that the same, or at least comparable polarization states should also be present in teleosts. However, corresponding transcriptional profiles of marker genes have not been reported thus far. In this study we confirm that macrophages from common carp can polarize into M1- and M2 phenotypes with conserved functions and corresponding transcriptional profiles compared to mammalian macrophages. Carp M1 macrophages show increased production of nitric oxide and a transcriptional profile with increased pro-inflammatory cytokines and mediators, including il6, il12 and saa. Carp M2 macrophages show increased arginase activity and a transcriptional profile with increased anti-inflammatory mediators, including cyr61, timp2b and tgm2b. Our RNA sequencing approach allowed us to list, in an unbiased manner, markers discriminating between M1 and M2 macrophages of teleost fish. We discuss the importance of our findings for the evaluation of immunostimulants for aquaculture and for the identification of gene targets to generate transgenic zebrafish for detailed studies on M1 and M2 macrophages. Above all, we discuss the striking degree of evolutionary conservation of macrophage polarization in a lower vertebrate.

    Over de verscheidenheid aan levensvormen; wanneer telt het individu mee?
    Scheer, H. van der; Blacquiere, T. - \ 2020
    Bijenhouden 14 (2020)2. - ISSN 1877-9786 - p. 7 - 8.
    Biologische diversiteit of kortweg biodiversiteit gaat over verscheidenheid aan levensvormen binnen een bepaald gebied. Die levensvormen worden op Wikipedia beschreven als soorten en genen. En onder gebieden worden genoemd een ecosysteem, een vegetatiezone (bioom) of een gehele planeet.
    Gel Trapping Enables Optical Spectroscopy of Single Solvated Conjugated Polymers in Equilibrium
    De Laar, Ties Van; Hooiveld, Ellard ; Higler, Ruben ; Scheer, Pieter Van Der; Sprakel, Joris - \ 2019
    ACS Nano 13 (2019)11. - ISSN 1936-0851 - p. 13185 - 13195.
    conjugated polymers - gel entrapment - photodynamics - single-molecule fluorescent lifetime imaging - single-molecule spectroscopy

    Single-molecule studies have provided a wealth of insight into the photophysics of conjugated polymers in the solid and desolvated state. Desolvating conjugated chains, e.g., by their embedding in inert solid matrices, invariably leads to chain collapse and the formation of intermolecular aggregates, which have a pronounced effect on their properties. By contrast, the luminescent properties of individual semiconducting polymers in their solvated and thermodynamic state remain largely unexplored. In this paper, we demonstrate a versatile gel trapping technique that enables the chemistry-free immobilization and interrogation of individual conjugated macromolecules, which retain a fully equilibrated conformation by contrast to conventional solid-state immobilization methods. We show how the technique can be used to record full luminescence spectra of single chains, to evaluate their time-resolved fluorescence, and to probe their photodynamics. Finally, we explore how the photophysics of different conjugated polymers is strongly affected by desolvation and chain collapse.

    Rigidochromic conjugated polymers carrying main-chain molecular rotors
    Scheer, Pieter Van Der; Zuijlen, Quintin van; Sprakel, Joris - \ 2019
    Chemical Communications 55 (2019)77. - ISSN 1359-7345 - p. 11559 - 11562.

    We design and prepare rigidochromic conjugated polymers that carry molecular rotors in the main chain. We show how a suitable design maintains the mechanosensitivity of the rotors upon incorporation into an extended π-conjugated system. Construction of donor-acceptor polymers enables their use as ratiometric probes for polymer micromechanics, which we evidence through micromechanical imaging of a phase-separated polymer blend.

    Chain length-dependent luminescence in acceptor-doped conjugated polymers
    Scheer, Pieter van der; Laar, Ties van de; Sprakel, Joris - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322 - 12 p.

    Semiconducting polymers doped with a minority fraction of energy transfer acceptors feature a sensitive coupling between chain conformation and fluorescence emission, that can be harnessed for advanced solution-based molecular sensing and diagnostics. While it is known that chain length strongly affects chain conformation, and its response to external cues, the effects of chain length on the emission patterns in chromophore-doped conjugated polymers remains incompletely understood. In this paper, we explore chain-length dependent emission in two different acceptor-doped polyfluorenes. We show how the binomial distribution of acceptor incorporation, during the probabilistic polycondensation reaction, creates a strong chain-length dependency in the optical properties of this class of luminescent polymers. In addition, we also find that the intrachain exciton migration rate is chain-length dependent, giving rise to additional complexity. Both effects combined, make for the need to develop sensoric conjugated polymers of improved monodispersity and chemical homogeneity, to improve the accuracy of conjugated polymer based diagnostic approaches.

    Two-dimensional crystals of star polymers : a tale of tails
    Bos, Inge ; Scheer, Pieter van der; Ellenbroek, Wouter G. ; Sprakel, Joris - \ 2019
    Soft Matter 15 (2019)4. - ISSN 1744-683X - p. 615 - 622.

    The formation of non-hexagonal crystalline structures by the organisation of colloidal nanoparticles often involves the use of complex particles with anisotropic shape or interactions or the imposition of non-uniform external fields. Here we explore how unusual symmetries can be created using experimentally realistic particles that interact through isotropic and purely repulsive potentials. In particular, we use simulations to explore the phase behavior of two-dimensional systems of star polymers. We uncover how the tail of the pair potential has a large role in dictating the phase behavior. Star polymers interacting in the far field with a Gaussian potential only form hexagonal phases, while an exponential tail gives rise to stable primitive oblique and honeycomb lattices. We identify the ratio in strength between long and short range interactions and the nature of the transition between these regimes as crucial parameters to predict when non-hexagonal crystals of star polymers can be stable. This leads to experimental design rules for creating star polymers which should exhibit unusual lattice formation.

    Circadian misalignment induces fatty acid metabolism gene profiles and compromises insulin sensitivity in human skeletal muscle
    Wefers, Jakob ; Moorsel, Dirk van; Hansen, Jan ; Connell, Niels J. ; Havekes, Bas ; Hoeks, Joris ; Marken Lichtenbelt, Wouter D. van; Duez, Hélène ; Phielix, Esther ; Kalsbeek, Andries ; Boekschoten, Mark V. ; Hooiveld, Guido J. ; Hesselink, Matthijs K.C. ; Kersten, Sander ; Staels, Bart ; Scheer, Frank A.J.L. ; Schrauwen, Patrick - \ 2018
    Proceedings of the National Academy of Sciences of the United States of America 115 (2018)30. - ISSN 0027-8424 - p. 7789 - 7794.
    Circadian misalignment, such as in shift work, has been associated with obesity and type 2 diabetes. However, direct effects of circadian misalignment on skeletal muscle insulin sensitivity and the muscle molecular circadian clock have never been studied in humans. Here, we investigated insulin sensitivity and muscle metabolism in 14 healthy young lean men [age 22.4 ± 2.8 years; body mass index (BMI) 22.3 ± 2.1 kg/m2 (mean ± SD)] after a 3-d control protocol and a 3.5-d misalignment protocol induced by a 12-h rapid shift of the behavioral cycle. We show that short-term circadian misalignment results in a significant decrease in muscle insulin sensitivity due to a reduced skeletal muscle nonoxidative glucose disposal (rate of disappearance: 23.7 ± 2.4 vs. 18.4 ± 1.4 mg/kg per minute; control vs. misalignment; P = 0.024). Fasting glucose and free fatty acid levels as well as sleeping metabolic rate were higher during circadian misalignment. Molecular analysis of skeletal muscle biopsies revealed that the molecular circadian clock was not aligned to the inverted behavioral cycle, and transcriptome analysis revealed the human PPAR pathway as a key player in the disturbed energy metabolism upon circadian misalignment. Our findings may provide a mechanism underlying the increased risk of type 2 diabetes among shift workers.
    Giving Voice to Patients : Developing a Discussion Method to Involve Patients in Translational Research
    Boenink, Marianne ; Scheer, Lieke van der; Garcia, Elisa ; Burg, Simone van der - \ 2018
    NanoEthics 12 (2018)3. - ISSN 1871-4757 - p. 181 - 197.
    Biomedical innovation - Discussion method - Experiential knowledge - Patient involvement - Research and development - Translational research

    Biomedical research policy in recent years has often tried to make such research more ‘translational’, aiming to facilitate the transfer of insights from research and development (R&D) to health care for the benefit of future users. Involving patients in deliberations about and design of biomedical research may increase the quality of R&D and of resulting innovations and thus contribute to translation. However, patient involvement in biomedical research is not an easy feat. This paper discusses the development of a method for involving patients in (translational) biomedical research aiming to address its main challenges. After reviewing the potential challenges of patient involvement, we formulate three requirements for any method to meaningfully involve patients in (translational) biomedical research. It should enable patients (1) to put forward their experiential knowledge, (2) to develop a rich view of what an envisioned innovation might look like and do, and (3) to connect their experiential knowledge with the envisioned innovation. We then describe how we developed the card-based discussion method ‘Voice of patients’, and discuss to what extent the method, when used in four focus groups, satisfied these requirements. We conclude that the method is quite successful in mobilising patients’ experiential knowledge, in stimulating their imaginaries of the innovation under discussion and to some extent also in connecting these two. More work is needed to translate patients’ considerations into recommendations relevant to researchers’ activities. It also seems wise to broaden the audience for patients’ considerations to other actors working on a specific innovation.

    Light from Within: Sensing Weak Strains and FemtoNewton Forces in Single Molecules
    Laar, Ties van de; Schuurman, Hent ; Scheer, Pieter van der; Maarten van Doorn, Jan ; Gucht, Jasper van der; Sprakel, Joris - \ 2018
    Chem 4 (2018)2. - ISSN 2451-9308 - p. 269 - 284.
    conjugated polymers - mechanochromism - molecular force sensors - single-molecule spectroscopy
    Weak mechanical forces acting on molecules are in control of a wide variety of (bio)chemical and physical processes. The spatially inhomogeneous nature of these forces has a profound effect on the structure and mechanics of soft and biological materials. Yet, the lack of methods for probing sub-picoNewton forces at high resolution leaves our understanding of these effects incomplete. Here, we solve this challenge by engineering semiconducting polymers to act as ultraweak force sensors. Combining simulations, chemical synthesis, and single-molecule fluorescence spectroscopy, we demonstrate force sensing in single molecules. We achieve grayscale force detection, at a resolution as low as 300 fN, down to the molecular scale. Our approach opens the way to illuminating and quantifying molecular mechanics with unprecedented resolution. Mechanical stress at the molecular scale plays a crucial role in a wide variety of (bio)chemical processes, ranging from the sensing of the mechanical environment by cells to the failure of high-tech engineering materials. Although we know these molecular forces exist, making them visible and quantifying them at the molecular scale have remained impossible to date. This lack of direct insight at the molecular level has precluded a deeper understanding of how mechanics govern these problems. Here, we demonstrate quantitative force sensing in individual molecules at an unprecedented force resolution. Our approach is completely non-invasive and thus opens the way to visualizing and quantifying mechanical stresses in molecular materials and complex biological scenarios. Weak forces acting on molecules govern a vast range of physical, chemical, and biological phenomena. To date, it has not been possible to measure these forces directly because force-sensing methods at the nanoscale have lacked the resolution to resolve ultraweak forces at the scale of single molecules deep within complex materials. Here, we solve this challenge by demonstrating single-molecule force sensing with engineered light-emitting molecules and reporting forces as small as one trillionth of a Newton.
    LNV en WUR: precisielandbouw bewijzen bij telers
    Booij, J.A. - \ 2017
    Vliegoefeningen voor bijen : bijen in de flight simulator
    Dooremalen, J.A. van; Scheer, H. van der - \ 2017
    Bijenhouden 11 (2017)1. - ISSN 1877-9786 - p. 30 - 31.
    Iemand heeft ooit berekend hoe groot de afstand is die een haalbij gedurende haar werkzame leven aflegt. Dat moet ongeveer 800 km zijn; ongetwijfeld een gemiddelde. Je zult als bij maar pech hebben en met misvormde vleugels (DWV) zijn geboren. Dan kom je niet ver. Nog een punt: die metingen zijn gedaan aan ogenschijnlijk gezonde, vitale honingbijen. Dat wil niet zeggen dat ze inderdaad gezond waren. Als wij bijen waren zouden we natuurlijk willen weten wie er nu kampioen is in het langeafstandvliegen en wie er het snelst is. Bijen doen daar niet aan mee. Die kennen geen kampioenen.
    Fragility and Strength in Nanoparticle Glasses
    Scheer, Pieter van der; Laar, Ties van de; Gucht, Jasper van der; Vlassopoulos, Dimitris ; Sprakel, Joris - \ 2017
    ACS Nano 11 (2017)7. - ISSN 1936-0851 - p. 6755 - 6763.
    colloids - fragility - glasses - microgels - nanoparticles

    Glasses formed from nano- and microparticles form a fascinating testing ground to explore and understand the origins of vitrification. For atomic and molecular glasses, a wide range of fragilities have been observed; in colloidal systems, these effects can be emulated by adjusting the particle softness. The colloidal glass transition can range from a superexponential, fragile increase in viscosity with increasing density for hard spheres to a strong, Arrhenius-like transition for compressible particles. However, the microscopic origin of fragility and strength remains elusive, both in the colloidal and in the atomic domains. Here, we propose a simple model that explains fragility changes in colloidal glasses by describing the volume regulation of compressible colloids in order to maintain osmotic equilibrium. Our simple model provides a microscopic explanation for fragility, and we show that it can describe experimental data for a variety of soft colloidal systems, ranging from microgels to star polymers and proteins. Our results highlight that the elastic energy per particle acts as an effective fragility order parameter, leading to a universal description of the colloidal glass transition.

    Doping. Een beetje vergif stimuleert.
    Scheer, H. van der; Blacquiere, T. - \ 2016
    Bijenhouden 10 (2016)6. - ISSN 1877-9786 - p. 24 - 26.
    Veel mensen nuttigen meerdere kopjes koffie per dag. Ze genieten van het giftige alkaloïde cafeïne, een natuurlijk insecticide en slakkengif dat planten aanmaken om zich te beschermen tegen vraat. Veel kopjes koffie per dag veroorzaken negatieve stemmingseffecten zoals angst. Een kopje koffie bevat ongeveer het tachtigste deel van een hoeveelheid cafeïne die dodelijk is voor de helft van de koffiedrinkers (LD50). Gelukkig beperkt men zich met drinken en kan het lichaam cafeïne redelijk snel afbreken en zo de schade beperken. Dat geldt ook voor nicotine bij rokers. In een pakje sigaretten zit genoeg nicotine om dodelijk te zijn bij eenmalig injecteren, maar via roken komt het geleidelijk binnen en wordt het relatief snel afgebroken. Bij geringe, subletale doseringen van genoemde vergiffen voelen veel mensen zich beter in staat tot werken, deels door de verslavende werking. Honingbijen houden, net als mensen van een beetje nicotine en cafeïne, maar dan in nectar.
    Overleven: op zoek naar bijenvolken die kunnen omgaan met varroa en verkreukeldevleugelvirus
    Blacquiere, T. ; Scheer, H. van der - \ 2016
    Bijenhouden 10 (2016)3. - ISSN 1877-9786 - p. 12 - 14.
    De Europese rassen van de westerse honingbij (Apis mellifera) zitten in Europa en Noord-Amerika al een tiental jaren in zwaar weer vanwege abnormale bijensterfte en het jaarlijks verlies van 20-30% van de volken (Van der Scheer en Blacquière, 2013b). Ook al is de besmetting met varroa in Nederland de laatste twee jaar minder, toch hebben de honingbijen nog veel last van de parasitaire varroamijt (Varroa destructor) in combinatie met het verkreukeldevleugelvirus, in het Engels Deformed Wing Virus, afgekort DWV (Van der Scheer en Blacquière, 2013a). Die besmetting met mijten vergt bestrijding om de volken in leven te houden. Omdat bestrijding veel aandacht vraagt en geld kost wordt er gezocht naar varroa-resistente volken van de westerse honingbij
    Biological control of apple scab (Venturia inaequalis) epidemics by Cladosporium cladosporioides H39
    Köhl, J. ; Scheer, C. ; Holb, I.J. ; Masny, S. ; Molhoek, W.M.L. - \ 2016
    In: Working Group "Biological and Integrated Control of Plant Pathogens". - IOBC-WPRS (IOBC-WPRS Bulletin ) - ISBN 9789290672999 - p. 213 - 215.
    Amsterdamse stadsfruit-projecten WUR uitgebreid
    Ravesloot, Marc - \ 2015
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