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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CCDC 1858109: Experimental Crystal Structure Determination
Keisar, Hodaya ; Ruiter, Graham de; Velders, A.H. ; Milko, Petr ; Gulino, Antonino ; Evmenenko, Guennadi ; Shimon, Linda J.W. ; Diskin-Posner, Yael ; Lahav, Michal ; Boom, Milko E. van der - \ 2018
PIHQEF : fac-tris{4-methyl-4'-[2-(pyridin-4-yl)ethenyl]-2,2'-bipyridine}-osmium bis(hexafluorophosphate) benzene toluene unknown solvate
CCDC 1858110: Experimental Crystal Structure Determination
Keisar, Hodaya ; Ruiter, Graham de; Velders, A.H. ; Milko, Petr ; Gulino, Antonino ; Evmenenko, Guennadi ; Shimon, Linda J.W. ; Diskin-Posner, Yael ; Lahav, Michal ; Boom, Milko E. van der - \ 2018
PIHQIJ : mer-tris{4-methyl-4'-[2-(pyridin-4-yl)ethenyl]-2,2'-bipyridine}-osmium bis(hexafluorophosphate) unknown solvate
CCDC 1858108: Experimental Crystal Structure Determination
Keisar, Hodaya ; Ruiter, Graham de; Velders, A.H. ; Milko, Petr ; Gulino, Antonino ; Evmenenko, Guennadi ; Shimon, Linda J.W. ; Lahav, Michal ; Boom, Milko E. van der - \ 2018
PIHQAB : tris{4-methyl-4'-[2-(pyridin-4-yl)ethenyl]-2,2'-bipyridine}-ruthenium bis(hexafluorophosphate) unknown solvate
Sorting of Molecular Building Blocks from Solution to Surface
Keisar, Hodaya ; Ruiter, Graham de; Velders, Aldrik H. ; Milko, Petr ; Gulino, Antonino ; Evmenenko, Guennadi ; Shimon, Linda J.W. ; Diskin-Posner, Yael ; Lahav, Michal ; Boom, Milko E. van der - \ 2018
Journal of the American Chemical Society 140 (2018)26. - ISSN 0002-7863 - p. 8162 - 8171.

We demonstrate that molecular gradients on an organic monolayer is formed by preferential binding of ruthenium complexes from solutions also containing equimolar amounts of isostructural osmium complexes. The monolayer consists of a nanometer-thick assembly of 1,3,5-tris(4-pyridylethenyl)benzene (TPEB) covalently attached to a silicon or metal-oxide surface. The molecular gradient of ruthenium and osmium complexes is orthogonal to the surface plane. This gradient propagates throughout the molecular assembly with thicknesses over 30 nm. Using other monolayers consisting of closely related organic molecules or metal complexes results in the formation of molecular assemblies having an homogeneous and equimolar distribution of ruthenium and osmium complexes. Spectroscopic and computational studies revealed that the geometry of the complexes and the electronic properties of their ligands are nearly identical. These subtle differences cause the isostructural osmium and ruthenium complexes to pack differently on modified surfaces as also demonstrated in crystals grown from solution. The different packing behavior, combined with the organic monolayer significantly contributes to the observed differences in chemical composition on the surface.

Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers
Ploetz, Evelyn ; Lerner, Eitan ; Husada, Florence ; Roelfs, Martin ; Chung, Sangyoon ; Hohlbein, Johannes ; Weiss, Shimon ; Cordes, Thorben - \ 2016
Scientific Reports 6 (2016). - ISSN 2045-2322

Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-Talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.

A Quantitative Theoretical Framework for Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET)
Lerner, Eitan ; Ploetz, Evelyn ; Hohlbein, Johannes ; Cordes, Thorben ; Weiss, Shimon - \ 2016
The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 120 (2016)26. - ISSN 1520-6106 - p. 6401 - 6410.

Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

Pyrrolizidine and tropane alkaloids in teas and the herbal teas peppermint, rooibos and chamomile in the Israeli market
Shimshoni, Jakob Avi ; Duebecke, Arne ; Mulder, Patrick P.J. ; Cuneah, Olga ; Barel, Shimon - \ 2015
Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 32 (2015)12. - ISSN 1944-0049 - p. 2058 - 2067.
herbal tea - LC-MS/MS - pyrrolizidine alkaloids - tea - tropane alkaloids

Dehydro pyrrolizidine alkaloids (dehydro PAs) are carcinogenic phytotoxins prevalent in the Boraginaceae, Asteraceae and Fabaceae families. Dehydro PAs enter the food and feed chain by co-harvesting of crops intended for human and animal consumption as well as by carry-over into animal-based products such as milk, eggs and honey. Recently the occurrence of dehydro PAs in teas and herbal teas has gained increasing attention from the EU, due to the high levels of dehydro PAs found in commercially available teas and herbal teas in Germany and Switzerland. Furthermore, several tropane alkaloids (TAs, e.g. scopolamine and hyoscyamine) intoxications due to the consumption of contaminated herbal teas were reported in the literature. The aim of the present study was to determine the dehydro PAs and TAs levels in 70 pre-packed teabags of herbal and non-herbal tea types sold in supermarkets in Israel. Chamomile, peppermint and rooibos teas contained high dehydro PAs levels in almost all samples analysed. Lower amounts were detected in black and green teas, while no dehydro PAs were found in fennel and melissa herbal teas. Total dehydro PAs concentrations in chamomile, peppermint and rooibos teas ranged from 20 to 1729 μg/kg. Except for black tea containing only mono-ester retrorsine-type dehydro PAs, all other teas and herbal teas showed mixed patterns of dehydro PA ester types, indicating a contamination by various weed species during harvesting and/or production. The TA levels per teabag were below the recommended acute reference dose; however, the positive findings of TAs in all peppermint tea samples warrant a more extensive survey. The partially high levels of dehydro PAs found in teas and herbal teas present an urgent warning letter to the regulatory authorities to perform routine quality control analysis and implement maximum residual levels for dehydro PAs.

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