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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Plastome based phylogenetics and younger crown node age in Pelargonium
Kerke, Sara J. van de; Shrestha, Bikash ; Ruhlman, Tracey A. ; Weng, Mao Lun ; Jansen, Robert K. ; Jones, Cynthia S. ; Schlichting, Carl D. ; Hosseini, Samin ; Mohammadin, Setareh ; Schranz, M.E. ; Bakker, Freek T. - \ 2019
Molecular Phylogenetics and Evolution 137 (2019). - ISSN 1055-7903 - p. 33 - 43.
Geraniaceae - Pelargonium - Phylogeny - Plastome - Time-calibrated

The predominantly South-African plant genus Pelargonium L'Hér. (Geraniaceae) displays remarkable morphological diversity, several basic chromosome numbers as well as high levels of organelle genomic rearrangements, and represents the 7th largest Cape Floristic Region clade. In this study, we reconstructed a phylogenetic tree based on 74 plastome exons and nuclear rDNA ITS regions for 120 species, which represents 43% taxon coverage for Pelargonium. We also performed a dating analysis to examine the timing of the major radiations in the genus. Phylogenetic analyses of nucleotide, amino acid, and ITS alignments confirmed the previously-documented subgeneric split into five main clades ((C1,C2),(B(A1,A2))) although clade only A1 received low bootstrap support. Using calibration evidence from a range of sources the Pelargonium crown age was estimated to be 9.7 My old, much younger than previous estimates for the genus but similar to recent studies of other Cape Floristic lineages that are part of both Fynbos and Succulent Karoo biomes.

Metabolic in Vivo Labeling Highlights Differences of Metabolically Active Microbes from the Mucosal Gastrointestinal Microbiome between High-Fat and Normal Chow Diet
Oberbach, Andreas ; Haange, Sven Bastiaan ; Schlichting, Nadine ; Heinrich, Marco ; Lehmann, Stefanie ; Till, Holger ; Hugenholtz, Floor ; Kullnick, Yvonne ; Smidt, Hauke ; Frank, Karin ; Seifert, Jana ; Jehmlich, Nico ; Bergen, Martin Von - \ 2017
Journal of Proteome Research 16 (2017)4. - ISSN 1535-3893 - p. 1593 - 1604.
16S rRNA gene sequencing - gut microbiota - metaproteomics - mucus layer - protein-based stable isotope probing
The gastrointestinal microbiota in the gut interacts metabolically and immunologically with the host tissue in the contact zone of the mucus layer. For understanding the details of these interactions and especially their dynamics it is crucial to identify the metabolically active subset of the microbiome. This became possible by the development of stable isotope probing techniques, which have only sparsely been applied to microbiome research. We applied the in vivo stable isotope approach using 15N-labeled diet with subsequent identification of metabolically active bacterial species. Four-week old male Sprague-Dawley rats were randomly assigned to chow diet (CD, n =15) and high-fat diet (HFD, n =15). After 11 weeks, three animals from each group were sacrificed for baseline characterization of anthropometric and metabolic obesity. The remaining animals were exposed to either a 15N-labeled (n =9) or a 14N-unlabeled experimental diet (n =3). Three rats from each cohort (HFD and CD) were sacrificed at 12, 24, and 72 h. The remaining three animals from each cohort, which received the 14N-unlabeled diet, were sacrificed after 72 h. The colon was harvested and divided into three equal sections (proximal, medial, and distal), and the mucus layer of each specimen was sampled by scraping. We identified the active subset in an HFD model of obesity in comparison with lean controls rats using metaproteomics. In addition, all samples were investigated by 16S rRNA amplicon gene sequencing. The active microbiome of the HFD group showed an increase in bacterial taxa for Verrucomicrobia and Desulfovibrionaceae. In contrast with no significant changes in alpha diversity, time- and localization-dependent effects in beta-diversity were clearly observed. In terms of enzymatic functions the HFD group showed strong affected metabolic pathways such as energy production and carbohydrate metabolism. In vivo isotope labeling combined with metaproteomics provides a valuable method to distinguish the active from the non-active bacterial phylogenetic groups that are relevant for microbiota-host interaction. For morbid obesity such analysis may provide potentially new strategies for targeted pre- or probiotic treatments.
Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities
Haange, S.B. ; Oberbach, A. ; Schlichting, N. ; Hugenholtz, F. ; Smidt, H. ; Bergen, M. van; Till, H. ; Seifert, J. - \ 2012
Journal of Proteome Research 11 (2012)11. - ISSN 1535-3893 - p. 5406 - 5417.
gut microbiota - superoxide reductase - escherichia-coli - host metabolism - fecal samples - bacteria - community - diversity - proteins - carbon
The digestion of food ingredients depends on the action of the gut microbiota and has a significant influence on the health, especially in the case of metabolic diseases, of the host organism. Despite the relevance of the structure and functionalities in the microbiota for the metabolism of the host, the spatial resolution of microbial consortia and the functionalities in the different gut sections of the rat are mostly unknown. Since there are suitable rat models for human metabolic diseases, the microbiota of the rat is of special interest. Samples along the intestinal tract of rats were investigated using metaproteomics and 16S rRNA gene pyrosequencing. The procedures for harvesting bacteria from the mucus and the content of the gut sections and feces were optimized leading to 2802 nonredundant bacterial protein groups in total that were assigned to spectra measured by liquid chromatography-tandem mass spectrometry. The majority of 16S rRNA genes and protein groups belonged to members of Firmicutes, Bacteroidetes and Proteobacteria. The functionalities in the enzyme repertoire were compared between the mucus and the content of the large intestine sections and the feces samples. This spatial resolution allowed pinpointing changes in the community to specific metabolic capacities like carbohydrate transport and energy conservation. The results showed that the mere analysis of feces samples reflects the functions of the gut microbiota only to a minor extent and sheds light on the metabolic interchange between the microbiota and the host organism.
Leaf shape evolution in the South African genus pelargonium l'Hèr. (Geraniaceae)
Jones, C.S. ; Bakker, F.T. ; Schlichting, C.D. ; Nicotra, A.B. - \ 2009
Evolution 63 (2009)2. - ISSN 0014-3820 - p. 479 - 497.
soil-nutrient gradients - cape flora - morphological evolution - bayesian-inference - phylogeny - leaves - diversity - venation - size - temperature
Leaf shapes reflect complex assemblages of shape-determining elements, yet evolutionary studies tend to treat leaf shape as a single attribute, for example cordate or linear. As with all complex structures, individual elements of a leaf could theoretically evolve independently and at different rates to the extent permitted by genetic and functional limitations. We examined relative evolutionary lability of shape-determining elements in the highly diverse South African plant genus Pelargonium (Geraniaceae). We used SIMMAP to calculate Bayesian posterior probabilities for ancestral states of leaf-shape characters for major nodes across multiple phylogenetic trees. Trees were derived from a Bayesian analysis of DNA sequence data from four partitions. We found that shape elements differed in rates of character-state transformations across the tree. Leaf base, apex, and overall outline had low rates. Transformations in venation occurred at slightly higher rates and were associated with shifts in venation among major clades. Leaf margin type and overall leaf size showed intermediate rates, whereas high rates were observed in the extent of lamina lobing and functional leaf size. The results indicate that suites of elements characteristic of the recently evolved xerophytic lineage, for example pinnate venation, dissected lamina, and entire margins, were acquired piecemeal over nested levels of the phylogeny
Charge transport in mesomorphic imido-substituted aromatic macrocycles
Craats, A.M. van der; Warman, J.M. ; Kimkes, P. ; Struijk, C.W. ; Zuilhof, H. ; Sudhölter, E.J.R. ; Schlichting, P. ; Rohr, U. ; Geerts, Y. ; Muellen, K. - \ 1999
In: Book of abstracts : Vloeibare kristallendag, Nijmegen, 4 mei 1999. - [S.l.] : [s.n.], 1999 - p. 19 - 19.
Ernst Schlichting und die Erforschung hydromorpher/reduktomorpher Boden.
Pons, L.J. - \ 1990
In: Ernst-Schlichting-Gedächtnis-Kolloquium; Tagungsband S.41-53
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