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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Far-red light during cultivation induces postharvest cold tolerance in tomato fruit
Affandi, Fahrizal Y. ; Verdonk, Julian C. ; Ouzounis, Theoharis ; Ji, Yongran ; Woltering, Ernst J. ; Schouten, Rob E. - \ 2020
Postharvest Biology and Technology 159 (2020). - ISSN 0925-5214
We investigated the role of far-red LED light during cultivation on postharvest cold tolerance in tomato fruit (Solanum lycopersicum cv Moneymaker). Red and blue top LED light, providing 150 μmol m−2 s-1 photo-synthetically active radiation (PAR) at plant height for 16 h daily, was combined with 0, 30 or 50 μmol m−2 s-1 (non-PAR) far-red LED light. Tomatoes were harvested at the mature green or red stage and subjected to cold storage for 0, 5, 10, and 15 d at 4 °C, followed by 20 d shelf-life at 20 °C.
Mature green harvested tomatoes, cultivated with additional far-red light, showed reduced weight loss, less pitting, faster red colour development during shelf-life (when prior long cold stored), and less softening (when prior short or non-cold stored). FR lighting during cultivation likely protects the membrane integrity of MG tomatoes and thus allows uninterrupted lycopene synthesis. Red harvested tomatoes cultivated with additional far-red light were firmer at harvest, showed reduced weight loss and less decay during shelf-life. Less red colouration was observed for red harvested fruits at the start of shelf-life when fruits were prior cold stored, indicative of lycopene breakdown during cold storage. The improved cold tolerance of red harvested fruits grown under additional far-red light is likely due to higher firmness at the start of the shelf-life period with lycopene acting as antioxidant during cold storage. In conclusion, additional far-red light during cultivation improved postharvest cold tolerance for tomatoes harvested at both the green and red maturity stage, and might therefore be suitable to prolong the storage potential of tomato at sub-optimal temperatures.
Nederland gidsland
Ende, Ernst van den - \ 2019
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, C.T. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo Da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology (2019). - ISSN 1087-0156

In the version of this article initially published, some reference citations were incorrect. The three references to Jupyter Notebooks should have cited Kluyver et al. instead of Gonzalez et al. The reference to Qiita should have cited Gonzalez et al. instead of Schloss et al. The reference to mothur should have cited Schloss et al. instead of McMurdie & Holmes. The reference to phyloseq should have cited McMurdie & Holmes instead of Huber et al. The reference to Bioconductor should have cited Huber et al. instead of Franzosa et al. And the reference to the biobakery suite should have cited Franzosa et al. instead of Kluyver et al. The errors have been corrected in the HTML and PDF versions of the article.

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools
Ernst, Madeleine ; Kang, Kyo Bin ; Caraballo-Rodríguez, Andrés Mauricio ; Nothias, Louis Felix ; Wandy, Joe ; Chen, Christopher ; Wang, Mingxun ; Rogers, Simon ; Medema, Marnix H. ; Dorrestein, Pieter C. ; Hooft, Justin J.J. van der - \ 2019
Metabolites 9 (2019)7. - ISSN 2218-1989
Chemical classification - In silico workflows - Metabolite annotation - Metabolite identification - Metabolome mining - Molecular families - Networking - Substructures

Metabolomics has started to embrace computational approaches for chemical interpretation of large data sets. Yet, metabolite annotation remains a key challenge. Recently, molecular networking and MS2LDA emerged as molecular mining tools that find molecular families and substructures in mass spectrometry fragmentation data. Moreover, in silico annotation tools obtain and rank candidate molecules for fragmentation spectra. Ideally, all structural information obtained and inferred from these computational tools could be combined to increase the resulting chemical insight one can obtain from a data set. However, integration is currently hampered as each tool has its own output format and efficient matching of data across these tools is lacking. Here, we introduce MolNetEnhancer, a workflow that combines the outputs from molecular networking, MS2LDA, in silico annotation tools (such as Network Annotation Propagation or DEREPLICATOR), and the automated chemical classification through ClassyFire to provide a more comprehensive chemical overview of metabolomics data whilst at the same time illuminating structural details for each fragmentation spectrum. We present examples from four plant and bacterial case studies and show how MolNetEnhancer enables the chemical annotation, visualization, and discovery of the subtle substructural diversity within molecular families. We conclude that MolNetEnhancer is a useful tool that greatly assists the metabolomics researcher in deciphering the metabolome through combination of multiple independent in silico pipelines.

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Bolyen, Evan ; Rideout, Jai Ram ; Dillon, Matthew R. ; Bokulich, Nicholas A. ; Abnet, Christian C. ; Al-Ghalith, Gabriel A. ; Alexander, Harriet ; Alm, Eric J. ; Arumugam, Manimozhiyan ; Asnicar, Francesco ; Bai, Yang ; Bisanz, Jordan E. ; Bittinger, Kyle ; Brejnrod, Asker ; Brislawn, Colin J. ; Brown, Titus C. ; Callahan, Benjamin J. ; Caraballo-Rodríguez, Andrés Mauricio ; Chase, John ; Cope, Emily K. ; Silva, Ricardo da; Diener, Christian ; Dorrestein, Pieter C. ; Douglas, Gavin M. ; Durall, Daniel M. ; Duvallet, Claire ; Edwardson, Christian F. ; Ernst, Madeleine ; Estaki, Mehrbod ; Fouquier, Jennifer ; Gauglitz, Julia M. ; Gibbons, Sean M. ; Gibson, Deanna L. ; Gonzalez, Antonio ; Gorlick, Kestrel ; Guo, Jiarong ; Hillmann, Benjamin ; Holmes, Susan ; Holste, Hannes ; Huttenhower, Curtis ; Huttley, Gavin A. ; Janssen, Stefan ; Jarmusch, Alan K. ; Jiang, Lingjing ; Kaehler, Benjamin D. ; Kang, Kyo Bin ; Keefe, Christopher R. ; Keim, Paul ; Kelley, Scott T. ; Knights, Dan ; Koester, Irina ; Kosciolek, Tomasz ; Kreps, Jorden ; Langille, Morgan G.I. ; Lee, Joslynn ; Ley, Ruth ; Liu, Yong Xin ; Loftfield, Erikka ; Lozupone, Catherine ; Maher, Massoud ; Marotz, Clarisse ; Martin, Bryan D. ; McDonald, Daniel ; McIver, Lauren J. ; Melnik, Alexey V. ; Metcalf, Jessica L. ; Morgan, Sydney C. ; Morton, Jamie T. ; Naimey, Ahmad Turan ; Navas-Molina, Jose A. ; Nothias, Louis Felix ; Orchanian, Stephanie B. ; Pearson, Talima ; Peoples, Samuel L. ; Petras, Daniel ; Preuss, Mary Lai ; Pruesse, Elmar ; Rasmussen, Lasse Buur ; Rivers, Adam ; Robeson, Michael S. ; Rosenthal, Patrick ; Segata, Nicola ; Shaffer, Michael ; Shiffer, Arron ; Sinha, Rashmi ; Song, Se Jin ; Spear, John R. ; Swafford, Austin D. ; Thompson, Luke R. ; Torres, Pedro J. ; Trinh, Pauline ; Tripathi, Anupriya ; Turnbaugh, Peter J. ; Ul-Hasan, Sabah ; Hooft, Justin J.J. van der; Vargas, Fernando ; Vázquez-Baeza, Yoshiki ; Vogtmann, Emily ; Hippel, Max von; Walters, William ; Wan, Yunhu ; Wang, Mingxun ; Warren, Jonathan ; Weber, Kyle C. ; Williamson, Charles H.D. ; Willis, Amy D. ; Xu, Zhenjiang Zech ; Zaneveld, Jesse R. ; Zhang, Yilong ; Zhu, Qiyun ; Knight, Rob ; Caporaso, J.G. - \ 2019
Nature Biotechnology 37 (2019)8. - ISSN 1087-0156 - p. 852 - 857.
Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l.
Ernst, Madeleine ; Nothias, Louis Félix ; Hooft, Justin J.J. van der; Silva, Ricardo R. ; Saslis-Lagoudakis, Haris C. ; Grace, Olwen M. ; Martinez-Swatson, Karen ; Hassemer, Gustavo ; Funez, Luís A. ; Simonsen, Henrik T. ; Medema, Marnix H. ; Staerk, Dan ; Nilsson, Niclas ; Lovato, Paola ; Dorrestein, Pieter C. ; Rønsted, Nina - \ 2019
Frontiers in Plant Science 10 (2019). - ISSN 1664-462X
Coevolution - Computational metabolomics - Euphorbia - Immunomodulatory testing - Specialized metabolites

Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic mosaic theory of coevolution predicts that coevolutionary interactions vary across geographic scales. Consequently, plant specialized metabolite diversity is expected to be highest in coevolutionary hotspots, geographic regions, which exhibit strong reciprocal selection on the interacting species. Despite being well-established theoretical frameworks, technical limitations have precluded rigorous hypothesis testing. Here we aim at understanding how geographic separation over evolutionary time may have impacted chemical differentiation in the cosmopolitan plant genus Euphorbia. We use a combination of state-of-the-art computational mass spectral metabolomics tools together with cell-based high-throughput immunomodulatory testing. Our results show significant differences in specialized metabolite diversity across geographically separated phylogenetic clades. Chemical structural diversity of the highly toxic Euphorbia diterpenoids is significantly reduced in species native to the Americas, compared to Afro-Eurasia. The localization of these compounds to young stems and roots suggest a possible ecological relevance in herbivory defense. This is further supported by reduced immunomodulatory activity in the American subclade as well as herbivore distribution patterns. We conclude that computational mass spectrometric metabolomics coupled with relevant ecological data provide a strong tool for exploring plant specialized metabolite diversity in a chemo-evolutionary framework.

Improved phosphoric acid recovery from sewage sludge ash using layer-by-layer modified membranes
Paltrinieri, Laura ; Remmen, Kirsten ; Müller, Barbara ; Chu, Liangyong ; Köser, Joachim ; Wintgens, Thomas ; Wessling, Matthias ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. - \ 2019
Journal of Membrane Science 587 (2019). - ISSN 0376-7388
Layer-by-layer - Phosphate recovery - Polyelectrolyte - Sewage sludge ash - Water treatment

We report an advanced treatment method for phosphoric acid recovery from leached sewage sludge ash. Layer-by-layer (LbL) polyelectrolyte deposition has been used as a tool to modify and convert a hollow ultrafiltration membrane into a nanofiltration (NF) LbL membrane for H3PO4 recovery. To build the LbL membrane, poly(styrenesulfonate) PSS was chosen as polyanion, while three different polycations were used: a permanently charged polyelectrolyte, poly(diallyldimethylammonium chloride), PDADMAC; a pH-dependent charged polyelectrolyte poly(allylamine hydrochloride), PAH; and a PAH modified with guanidinium groups (PAH-Gu). Based on detailed surface characterizations (AFM, XPS and Zeta-potential) it was concluded that both charge density and pH-responsiveness of the polycations are key parameters to control the final membrane surface structure and transport properties. The surface properties of LbL-coated membranes were correlated with the membrane filtration performance, when exposed to the real leached sewage sludge ash solution. The highest permeability was recorded for (PDADMAC/PSS)6, a result that was rationalized on its loose, and possibly less interpenetrated, structure, followed by (PAH-Gu/PSS)6 characterized by a more dense, compact layer. H3PO4 recovery was the highest in the case of (PDADMAC/PSS)6, but the retention of multivalent metals (Fe3+ and Mg2+) was low, leading to a more contaminated permeate. The opposite trend was observed for (PAH-Gu/PSS)6, resulting in a less metal-contaminated, but also a less H3PO4-concentrated permeate. Our LbL-modified membranes were found to improve the permeability and H3PO4 recovery compared to a commercially available acid-resistant NF membrane.

Cell death signaling and morphology in chemical-treated tobacco BY-2 suspension cultured cells
Iakimova, Elena T. ; Yordanova, Zhenia P. ; Cristescu, Simona M. ; Harren, Frans J.M. ; Woltering, Ernst J. - \ 2019
Environmental and Experimental Botany 164 (2019). - ISSN 0098-8472 - p. 157 - 169.
Cell death - Ethylene - Lipid signaling - Reactive oxygen species - Tobacco BY-2 cells

This study addressed the role of lipid-derived factors together with ethylene and ROS in programmed cell death (PCD) signaling in tobacco BY-2 suspension cultured cells. The cells were exposed to the chemical stress agents mastoparan (MP) and ethanol (EtOH). MP is an activator of membrane-associated heterotrimeric G-proteins and downstream phospholipids-dependent processes; EtOH is suggested to affect lipid-associated pathways. The effects of MP and EtOH were compared to cell death in response to CdSO4. All applied chemicals appeared potent cell death inducers. Ethylene and lipid signaling were found instrumental in chemical-induced cell death, presumably in conjunction with ROS. Cadmium and MP induced cell death of apoptotic-like phenotype. Lower EtOH concentrations (1–2%) induced vacuolar cell death associated with autophagy-associated formation of lysosome-like acidic organelles in part of the cells; in other cells in the same suspension apoptotic-like features were observed. At higher EtOH concentration (3%) the dead cells expressed exclusively apoptotic-like morphology. The results suggest that phospholipase D- and phospholipase C-derived phosphatidic acid triggers ROS generation that is responsible for the observed apoptotic-like PCD. Vacuolar cell death in EtOH-treated cells appeared dependent on phospholipase C - phosphatidylinositol-3-kinase-related pathway. The obtained results indicate that depending on the inducer and stress severity, similar or distinct regulatory pathways can be activated, and the signals may interact in the transmission of the cell death message.

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra
Rogers, Simon ; Wei Ong, Cher ; Wandy, Joe ; Ernst, Madeleine ; Ridder, Lars ; Hooft, Justin J.J. Van Der - \ 2019
Faraday Discussions 218 (2019). - ISSN 1359-6640 - p. 284 - 302.
Complex metabolite mixtures are challenging to unravel. Mass spectrometry (MS) is a widely used and sensitive technique to obtain structural information on complex mixtures. However, just knowing the molecular masses of the mixture’s constituents is almost always insufficient for confident assignment of the associated chemical structures. Structural information can be augmented through MS fragmentation experiments whereby detected metabolites are fragmented giving rise to MS/MS spectra. However, how can we maximize the structural information we gain from fragmentation spectra? We recently proposed a substructure-based strategy to enhance metabolite annotation for complex mixtures by considering metabolites as the sum of (bio)chemically relevant moieties that we can detect through mass spectrometry fragmentation approaches. Our MS2LDA tool allows us to discover - unsupervised - groups of mass fragments and/or neutral losses termed Mass2Motifs that often correspond to substructures. After manual annotation, these Mass2Motifs can be used in subsequent MS2LDA analyses of new datasets, thereby providing structural annotations for many molecules that are not present in spectral databases. Here, we describe how additional strategies, taking advantage of i) combinatorial in-silico matching of experimental mass features to substructures of candidate molecules, and ii) automated machine learning classification of molecules, can facilitate semi-automated annotation of substructures. We show how our approach accelerates the Mass2Motif annotation process and therefore broadens the chemical space spanned by characterized motifs. Our machine learning model used to classify fragmentation spectra learns the relationships between fragment spectra and chemical features. Classification prediction on these features can be aggregated for all molecules that contribute to a particular Mass2Motif and guide Mass2Motif annotations. To make annotated Mass2Motifs available to the community, we also present motifDB: an open database of Mass2Motifs that can be browsed and accessed programmatically through an API. MotifDB is integrated within ms2lda.org, allowing users to efficiently search for characterized motifs in their own experiments. We expect that with an increasing number of Mass2Motif annotations available through a growing database we can more quickly gain insight in the constituents of complex mixtures. That will allow prioritization towards novel or unexpected chemistries and faster recognition of known biochemical building blocks.
Hightech ontmoet agrifood: WUR en TU Eindhoven werken steeds meer samen
Ende, Ernst van den - \ 2019
Molecular separation using poly (styrene-co-maleic anhydride) grafted to γ-alumina : Surface versus pore modification
Amirilargani, Mohammad ; Merlet, Renaud B. ; Chu, Liangyong ; Nijmeijer, Arian ; Winnubst, Louis ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. - \ 2019
Journal of Membrane Science 582 (2019). - ISSN 0376-7388 - p. 298 - 306.
Alumina membrane - Copolymer grafting - Molecular separation - Pore modification - Surface modification

Here, we report the covalent coupling of poly (styrene-co-maleic anhydride) onto γ-alumina to develop high-performance organic solvent nanofiltration (OSN) membranes. A high molecular weight (M w ) alternating copolymer of maleic anhydride (MA) and styrene (St) was synthesized and directly grafted to the γ-alumina membrane, while commercially available low M w random copolymers of St and MA were also investigated. We show that solute rejection and membrane permeability strongly depend on the nature of the applied copolymer. In particular, the M w of the copolymer applied is potentially the key for improving the membrane performance. When a high M w copolymer was applied, the grafted layer covered the surface of the membrane. This results in membranes with significantly improved rejection, while maintaining a high permeability. In contrast, we observed pore grafting by applying low M w copolymers, which resulted in membranes with slightly higher rejection and dramatically lower permeability compared to unmodified membrane. The best results were obtained by grafting γ-alumina with a high M w alternating copolymer. These membranes showed a solute rejection of 98% for Sudan Black B (457 g mol −1 ) in toluene, while the permeability remained high at 2.9 L m −2 h −1 bar −1 .

MIL-53(Al) and NH2-MIL-53(Al) modified α-alumina membranes for efficient adsorption of dyes from organic solvents
Amirilargani, Mohammad ; Merlet, Renaud B. ; Hedayati, Pegah ; Nijmeijer, Arian ; Winnubst, Louis ; Smet, Louis C.P.M. De; Sudhölter, Ernst J.R. - \ 2019
Chemical Communications 55 (2019)28. - ISSN 1359-7345 - p. 4119 - 4122.

To the best of our knowledge, for the first time MIL-53(Al) and NH 2 -MIL-53(Al) modified α-alumina membranes are investigated for the adsorption of organic dyes from organic solvents. These new, modified membranes show excellent adsorption of high concentrations of Rose Bengal dye in methanol and isopropanol solutions.

De novo construction of polyploid linkage maps using discrete graphical models
Behrouzi, Pariya ; Wit, Ernst C. - \ 2019
Bioinformatics 35 (2019)7. - ISSN 1367-4803 - p. 1083 - 1093.

Motivation Linkage maps are used to identify the location of genes responsible for traits and diseases. New sequencing techniques have created opportunities to substantially increase the density of genetic markers. Such revolutionary advances in technology have given rise to new challenges, such as creating high-density linkage maps. Current multiple testing approaches based on pairwise recombination fractions are underpowered in the high-dimensional setting and do not extend easily to polyploid species. To remedy these issues, we propose to construct linkage maps using graphical models either via a sparse Gaussian copula or a non-paranormal skeptic approach. Results We determine linkage groups, typically chromosomes, and the order of markers in each linkage group by inferring the conditional independence relationships among large numbers of markers in the genome. Through simulations, we illustrate the utility of our map construction method and compare its performance with other available methods, both when the data are clean and contain no missing observations and when data contain genotyping errors. Our comprehensive map construction method makes full use of the dosage SNP data to reconstruct linkage map for any bi-parental diploid and polyploid species. We apply the proposed method to three genotype datasets: Barley, peanut and potato from diploid and polyploid populations.

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae
Kang, Kyo Bin ; Ernst, Madeleine ; Hooft, Justin J.J. van der; Silva, Ricardo R. da; Park, Junha ; Medema, Marnix H. ; Sung, Sang Hyun ; Dorrestein, Pieter C. - \ 2019
The Plant Journal (2019). - ISSN 0960-7412
annotation - classification - mass spectrometry - Rhamnaceae - specialized metabolites - technical advance

Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped the diversity of specialized metabolites, which then drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating the diversity of specialized metabolites in an evolutionary context have been limited by the impossibility of identifying chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites and apply it to over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5% based on spectral library matches alone to 42.6% of total MS/MS molecular features, extending annotations from well-known plant compound classes into dark plant metabolomics. To gain insights into substructural diversity within this plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations for the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms.

Multicore Liquid Perfluorocarbon-Loaded Multimodal Nanoparticles for Stable Ultrasound and 19F MRI Applied to In Vivo Cell Tracking
Koshkina, Olga ; Lajoinie, Guillaume ; Baldelli Bombelli, Francesca ; Swider, Edyta ; Cruz, Luis J. ; White, Paul B. ; Schweins, Ralf ; Dolen, Yusuf ; Dinther, Eric A.W. van; Riessen, N.K. van; Rogers, Sarah E. ; Fokkink, Remco ; Voets, Ilja K. ; Eck, Ernst R.H. van; Heerschap, Arend ; Versluis, Michel ; Korte, Chris L. de; Figdor, Carl G. ; Vries, I.J.M. de; Srinivas, Mangala - \ 2019
Advanced Functional Materials 29 (2019)19. - ISSN 1616-301X
F MRI - cell therapy - cell tracking - multimodal imaging - perfluorocarbons - ultrasound

Ultrasound is the most commonly used clinical imaging modality. However, in applications requiring cell-labeling, the large size and short active lifetime of ultrasound contrast agents limit their longitudinal use. Here, 100 nm radius, clinically applicable, polymeric nanoparticles containing a liquid perfluorocarbon, which enhance ultrasound contrast during repeated ultrasound imaging over the course of at least 48 h, are described. The perfluorocarbon enables monitoring the nanoparticles with quantitative 19 F magnetic resonance imaging, making these particles effective multimodal imaging agents. Unlike typical core–shell perfluorocarbon-based ultrasound contrast agents, these nanoparticles have an atypical fractal internal structure. The nonvaporizing highly hydrophobic perfluorocarbon forms multiple cores within the polymeric matrix and is, surprisingly, hydrated with water, as determined from small-angle neutron scattering and nuclear magnetic resonance spectroscopy. Finally, the nanoparticles are used to image therapeutic dendritic cells with ultrasound in vivo, as well as with 19 F MRI and fluorescence imaging, demonstrating their potential for long-term in vivo multimodal imaging.

Ernst van den Ende: De gmo richtlijn moet worden aangepast
Ende, Ernst van den - \ 2019
Ernst van den Ende : ‘The GMO directive needs to be amended’
Ende, Ernst van den - \ 2019
Removing the no-analogue bias in modern accelerated tree growth leads to stronger medieval drought
Scharnweber, Tobias ; Heußner, Karl Uwe ; Smiljanic, Marko ; Heinrich, Ingo ; Maaten-Theunissen, Marieke van der; Maaten, Ernst van der; Struwe, Thomas ; Buras, Allan ; Wilmking, Martin - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

In many parts of the world, especially in the temperate regions of Europe and North-America, accelerated tree growth rates have been observed over the last decades. This widespread phenomenon is presumably caused by a combination of factors like atmospheric fertilization or changes in forest structure and/or management. If not properly acknowledged in the calibration of tree-ring based climate reconstructions, considerable bias concerning amplitudes and trends of reconstructed climatic parameters might emerge or low frequency information is lost. Here we present a simple but effective, data-driven approach to remove the recent non-climatic growth increase in tree-ring data. Accounting for the no-analogue calibration problem, a new hydroclimatic reconstruction for northern-central Europe revealed considerably drier conditions during the medieval climate anomaly (MCA) compared with standard reconstruction methods and other existing reconstructions. This demonstrates the necessity to account for fertilization effects in modern tree-ring data from affected regions before calibrating reconstruction models, to avoid biased results.

A Low-Power MEMS IDE Capacitor with Integrated Microhotplate : Application as Methanol Sensor using a Metal-Organic Framework Coating as Affinity Layer
Venkatesh, Manjunath R. ; Sachdeva, Sumit ; Mansouri, Brahim El; Wei, Jia ; Bossche, Andre ; Bosma, Duco ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. ; Zhang, Guo Qi - \ 2019
Sensors 19 (2019)4. - ISSN 1424-8220
Capacitor interdigitated electrodes - MEMS microhotplate - ZIF-8

Capacitors made of interdigitated electrodes (IDEs) as a transducer platform for the sensing of volatile organic compounds (VOCs) have advantages due to their lower power operation and fabrication using standard micro-fabrication techniques. Integrating a micro-electromechanical system (MEMS), such as a microhotplate with IDE capacitor, further allows study of the temperature- dependent sensing response of VOCs. In this paper, the design, fabrication, and characterization of a low-power MEMS microhotplate with IDE capacitor to study the temperature-dependent sensing response to methanol using Zeolitic imidazolate framework (ZIF-8), a class of metal-organic framework (MOF), is presented. A Titanium nitride (TiN) microhotplate with aluminum IDEs suspended on a silicon nitride membrane is fabricated and characterized. The power consumption of the ZIF-8 MOF-coated device at an operating temperature of 50 ∘ C is 4.5 mW and at 200 ∘ C it is 26 mW. A calibration methodology for the effects of temperature of the isolation layer between the microhotplate electrodes and the capacitor IDEs is developed. The device coated with ZIF-8 MOF shows a response to methanol in the concentration range of 500 ppm to 7000 ppm. The detection limit of the sensor for methanol vapor at 20 ∘ C is 100 ppm. In situ study of sensing properties of ZIF-8 MOF to methanol in the temperature range from 20 ∘ C to 50 ∘ C using the integrated microhotplate and IDE capacitor is presented. The kinetics of temperature-dependent adsorption and desorption of methanol by ZIF-8 MOF are fitted with double-exponential models. With the increase in temperature from 20 ∘ C to 50 ∘ C, the response time for sensing of methanol vapor concentration of 5000 ppm decreases by 28%, whereas the recovery time decreases by 70%.

Growing to shrink: Nano-tunable polystyrene brushes inside 5 nm mesopores
Merlet, Renaud B. ; Amirilargani, Mohammad ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. ; Nijmeijer, Arian ; Winnubst, Louis - \ 2019
Journal of Membrane Science 572 (2019). - ISSN 0376-7388 - p. 632 - 640.
ARGET ATRP - Gamma alumina - Inorganic membrane - Organic solvent nanofiltration - Polystyrene brush

The development of controlled polymerization techniques in the last decade has enabled polymer brushes to be grown from inorganic substrates with precision. Less studied are brushes grown from concave geometries of high curvature, such as mesopores, despite their application potential in the separation sciences. The method used here, surface-initiated, activators-regenerated-by-electron-transfer, atom-transfer radical polymerization (SI-ARGET-ATRP), is used to grow a polystyrene brush grown from aluminum oxide pores of 5 nm diameter, to-date the most confined geometry in which ATRP has been conducted. The brush is characterized by TGA, AFM, and FTIR, the latter two methods applied specifically to the external brush. Additionally, permporometry as well as permeability and retention measurements are used to characterize the graft within the mesopores. We show that the brush length is tunable, that the brush length is solvent-dependent, and we also demonstrate the application potential of this hybrid material as an organic solvent nanofiltration membrane. This new class of membranes shows excellent performance: a toluene permeability of 2.0 L m−2 h−1 bar−1 accompanied by a 90% rejection of diphenylanthracene (MW 330 g mol−1).

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