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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    In vivo analysis of formin dynamics in the moss P. patens reveals functional class diversification
    Gisbergen, Peter Van; Wu, Shu Zon ; Cheng, Xiaohang ; Pattavina, Kelli A. ; Bezanilla, Magdalena - \ 2020
    Journal of Cell Science 133 (2020)3. - ISSN 0021-9533
    Actin - Endocytosis - Exocytosis - Formin - Microtubule - Plant

    Formins are actin regulators critical for diverse processes across eukaryotes. With many formins in plants and animals, it has been challenging to determine formin function in vivo. We found that the phylogenetically distinct class I integral membrane formins (denoted For1) from the moss P. patens enrich at sites of membrane turnover, with For1D more tightly associated with the plasma membrane than For1A. To probe formin function, we generated formin-null lines with greatly reduced formin complexity. We found that For1A and For1D help to anchor actin near the cell apex, with For1A contributing to formation of cytosolic actin, while For1D contributes to plasma membrane-associated actin. At the cortex, For1A and For1D localized to motile puncta and differentially impacted actin dynamics. We found that class I cortical formin mobility depended on microtubules and only moderately on actin, whereas class II formin (denoted For2) mobility solely depended on actin. Moreover, cortical For2A tightly correlated with the puncta labeled by the endocytic membrane dye FM4-64, and null mutants in class I formins did not affect uptake of a similar dye, FM1-43, suggesting that class I and II formins are involved in distinct membrane trafficking pathways.

    Iron, zinc and phytic acid retention of biofortified, low phytic acid, and conventional bean varieties when preparing common household recipes
    Hummel, Marijke ; Talsma, Elise F. ; Taleon, Victor ; Londoño, Luis ; Brychkova, Galina ; Gallego, Sonia ; Raatz, Bodo ; Spillane, Charles - \ 2020
    Nutrients 12 (2020)3. - ISSN 2072-6643
    Anti-nutritionals - Beans - Biofortification - Cooking - Lpa - Micronutrients - Nutrition - Phaseolus vulgaris - Plant - Retention - SDG2

    Biofortification is an effective method to improve the nutritional content of crops and nutritional intake. Breeding for higher micronutrient mineral content in beans is correlated with an increase in phytic acid, a main inhibitor of mineral absorption in humans. Low phytic acid (lpa) beans have a 90% lower phytic acid content compared to conventional beans. This is the first study to investigate mineral and total phytic acid retention after preparing common household recipes from conventional, biofortified and lpa beans. Mineral retention was determined for two conventional, three biofortified and two lpa bean genotypes. Treatments included soaking, boiling (boiled beans) and refrying (bean paste). The average true retention of iron after boiling was 77.2– 91.3%; for zinc 41.2–84.0%; and for phytic acid 49.9–85.9%. Soaking led to a significant decrease in zinc and total phytic acid after boiling and refrying, whereas for iron no significant differences were found. lpa beans did not exhibit a consistent pattern of difference in iron and phytic acid retention compared to the other groups of beans. However, lpa beans had a significantly lower retention of zinc compared to conventional and biofortified varieties (p < 0.05). More research is needed to understand the underlying factors responsible for the differences in retention between the groups of beans, especially the low retention of zinc. Combining the lpa and biofortification traits could further improve the nutritional benefits of biofortified beans, by decreasing the phytic acid:iron and zinc ratio in beans.

    Genomic identification and analysis of specialized metabolite biosynthetic gene clusters in plants using plantiSMASH
    Kautsar, Satria A. ; Suarez Duran, Hernando G. ; Medema, Marnix H. - \ 2018
    In: Plant Chemical Genomics / Fauser, Friedrich, Jonikas, Martin, New York : Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493978731 - p. 173 - 188.
    Bioinformatics - Biosynthetic gene cluster - Biosynthetic pathway - Genomic - Plant - Secondary metabolite - Specialized metabolite

    Plants produce a vast diversity of specialized metabolites, which play important roles in the interactions with their microbiome, as well as with animals and other plants. Many such molecules have valuable biological activities that render them (potentially) useful as medicines, flavors and fragrances, nutritional ingredients, or cosmetics. Recently, plant scientists have discovered that the genes for many biosynthetic pathways for the production of such specialized metabolites are physically clustered on the chromosome within biosynthetic gene clusters (BGCs). The Plant Secondary Metabolite Analysis Shell (plantiSMASH) allows for the automated identification of such plant BGCs, facilitates comparison of BGCs across genomes, and helps users to predict the functional interactions of pairs of genes within and between BGCs based on coexpression analysis. In this chapter, we provide a detailed protocol on how to install and run plantiSMASH, and how to interpret its results to draw biological conclusions that are supported by the data.

    3C in maize and arabidopsis
    Weber, Blaise ; Jamge, Suraj ; Stam, Maike - \ 2018
    In: Plant Chromatin Dynamics / Bemer, M., Baroux, C., Humana Press Inc. (Methods in Molecular Biology ) - ISBN 9781493973170 - p. 247 - 270.
    3C protocol - Arabidopsis thaliana - Chromosome Conformation Capture - Plant - Zea mays
    With Chromosome Conformation Capture (3C), the relative interaction frequency of one chromosomal fragment with another can be determined. The technique is especially suited for unraveling the 3D organization of specific loci when focusing on aspects such as enhancer–promoter interactions or other topological conformations of the genome. 3C has been extensively used in animal systems, among others providing insight into gene regulation by distant cis-regulatory elements. In recent years, the 3C technique has been applied in plant research. However, the complexity of plant tissues prevents direct application of existing protocols from animals. Here, we describe an adapted protocol suitable for plant tissues, especially Arabidopsis thaliana and Zea mays.
    Polyploidy in deep and shallow evolutionary times : from ancient cotton, middle aged tobacco to recently formed monkey-flowers
    Kovarik, Ales ; Besendorfer, Višnja ; Plohl, Miroslav ; Schranz, Eric - \ 2017
    Plant Systematics and Evolution (2017). - ISSN 0378-2697 - 3 p.
    Biodiversity - Biological databases - Ecology - Evolution - Genetic variation - Hybridization - Plant - Polyploidy
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