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.
Handhavingsprotocol Hokverrijking : Praktische uitwerking van open normen in wetgeving helpt varkenswelzijn vooruit
Jonge, Francien de; Nieuwenhuizen, Jeroen van den; Ekkelboom, Myra ; Ernst, Kristi ; Kerssen, Nynke ; Smeets, Sharine ; Sun, Yan ; Yin, Xuetong ; Blaauw, Xana ; He, Zhengxiao ; Jong, Mandy de; Nauta, Charlotte ; Verdaasdonk, Marleen ; Kanhailal, Sharita - \ 2019
Wageningen : Wageningen University & Research, Wetenschapswinkel (Rapport / Wageningen University & Research, Wetenschapswinkel 353) - ISBN 9789463951685 - 27
Melamine-Based Microporous Organic Framework Thin Films on an Alumina Membrane for High-Flux Organic Solvent Nanofiltration
Amirilargani, Mohammad ; Yokota, Giovana N. ; Vermeij, Gijs H. ; Merlet, Renaud B. ; Delen, Guusje ; Mandemaker, Laurens D.B. ; Weckhuysen, Bert M. ; Winnubst, Louis ; Nijmeijer, Arian ; Smet, Louis C.P.M. de; Sudhölter, Ernst J.R. - \ 2019
ChemSusChem (2019). - ISSN 1864-5631
membranes - microporous materials - organic solvent nanofiltration - polymers - porous organic frameworks

Microporous polymer frameworks have attracted considerable attention to make novel separation layers owing to their highly porous structure, high permeability, and excellent molecular separation. This study concerns the fabrication and properties of thin melamine-based microporous polymer networks with a layer thickness of around 400 nm, supported on an α-alumina support and their potential use in organic solvent nanofiltration. The modified membranes show excellent solvent purification performances, such as n-heptane permeability as high as 9.2 L m−2 h−1 bar −1 in combination with a very high rejection of approximately 99 % for organic dyes with molecular weight of ≥457 Da. These values are higher than for the majority of the state-of-the-art membranes. The membranes further exhibit outstanding long-term operation stability. This work significantly expands the possibilities of using ceramic membranes in organic solvent nanofiltration.

Ripening of plum fruit : GreenCHAINge Fruit & Vegetables WP6
Woltering, Ernst ; Paillart, Maxence - \ 2019
Wageningen : Wageningen Food & Biobased Research (Report / Wageningen Food & Biobased Research 1972) - 15
Ripening of plums, from South Africa (SA), was studied following reefer transportation. In experiment 1, plum cultivars ‘Pioneer’ and ‘African Rose’ were ripened using different temperature scenarios. Both cultivars showed increased coloration during ripening, but this was much more pronounced in ‘Pioneer’ compared to ‘African Rose’. In ‘Pioneer’ there was a clear decrease in firmness during ripening; this was correlated with the temperature sum. At a temperature sum of 100-120 degree-days, the fruit had soften completely and reached the “ready–to-eat” stage. Increasing the temperature sum did not further soften the fruit. Irrespective the temperature scenario, ‘African Rose’ showed no softening and did not become “ready-to-eat”. In experiment 2, plum cultivars ‘ So ngold’ and ‘Southern Belle’ were harvested three times during their production season, transported to the Netherlands (NL), and ripening was studied at three temperatures (16, 20 and 24°C for 2 days). ‘So ngold’ was always less firm at arrival compared to ‘Southern Belle’. The applied temperatures did not have a clear effect on the speed of ripening. Fruit firmness at arrival was similar for the different batches of each cultivar; fruit from later harvest batches showed slightly more softening during storage and shelf life than fruit from first harvestbatch. Ethylene treatment (100 ppm, 24h) had effect on firmness loss in ‘Southern Belle’ when plums were ripened at higher temperature (ethylene effect was not tested in ‘So ngold’). Ethylene production in ‘Songold’ was about ten times higher than in ‘Southern Belle’ and increased during ripening in both cultivars. No clear effect of ripening temperature on ethylene production was observed.
Predicting strawberry shelf life based on input quality : GreenCHAINge Fruit & Vegetables WP3
Brouwer, Bastiaan ; Mensink, Manon ; Woltering, Ernst ; Pereira da Silva, Fatima - \ 2019
Wageningen : Wageningen Food & Biobased Research (Report / Wageningen Food & Biobased Research 1912) - 31
Dynamics of ripening of avocado fruit : GreenCHAINge Fruit & Vegetables WP6
Woltering, Ernst ; Paillart, Maxence - \ 2019
Wageningen : Wageningen Food & Biobased Research (Rapport / Wageningen Food & Biobased Research 1924) - 22
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.

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