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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    Genomics spurs rapid advances in our understanding of the biology of vascular wilt pathogens in the genus Verticillium
    Klimes, A. ; Dobinson, K.F. ; Thomma, B. ; Klosterman, S.J. - \ 2015
    Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 181 - 198.
    protein-kinase gene - molecular characterization - functional-analysis - microsclerotia development - ethylene perception - hydrophobin gene - dahliae kleb - tomato ve1 - resistance - expression
    The availability of genomic sequences of several Verticillium species triggered an explosion of genome-scale investigations of mechanisms fundamental to the Verticillium life cycle and disease process. Comparative genomics studies have revealed evolutionary mechanisms, such as hybridization and interchromosomal rearrangements, that have shaped these genomes. Functional analyses of a diverse group of genes encoding virulence factors indicate that successful host xylem colonization relies on specific Verticillium responses to various stresses, including nutrient deficiency and host defense–derived oxidative stress. Regulatory pathways that control responses to changes in nutrient availability also appear to positively control resting structure development. Conversely, resting structure development seems to be repressed by pathways, such as those involving effector secretion, which promote responses to host defenses. The genomics-enabled functional characterization of responses to the challenges presented by the xylem environment, accompanied by identification of novel virulence factors, has rapidly expanded our understanding of niche adaptation in Verticillium species.
    Investigations into the biosynthesis, regulation, and self-resistance of toxoflavin in Pseudomonas protegens Pf-5
    Philmus, B. ; Shaffer, B.T. ; Kidarsa, T.A. ; Yan, Q. ; Raaijmakers, J.M. ; Begley, T.P. ; Loper, J.E. - \ 2015
    ChemBioChem 16 (2015)12. - ISSN 1439-4227 - p. 1782 - 1790.
    formylglycine-generating enzyme - fluorescens pf-5 - burkholderia-glumae - pyoluteorin - cocovenenans - expression - oxidation - system - rice - gaca
    Pseudomonas spp. are prolific producers of natural products from many structural classes. Here we show that the soil bacterium Pseudomonas protegens Pf-5 is capable of producing trace levels of the triazine natural product toxoflavin (1) under microaerobic conditions. We evaluated toxoflavin production by derivatives of Pf-5 with deletions in specific biosynthesis genes, which led us to propose a revised biosynthetic pathway for toxoflavin that shares the first two steps with riboflavin biosynthesis. We also report that toxM, which is not present in the well-characterized cluster of Burkholderia glumae, encodes a monooxygenase that degrades toxoflavin. The toxoflavin degradation product of ToxM is identical to that of TflA, the toxoflavin lyase from Paenibacillus polymyxa. Toxoflavin production by P. protegens causes inhibition of several plant-pathogenic bacteria, and introduction of toxM into the toxoflavin-sensitive strain Pseudomonas syringae DC3000 results in resistance to toxoflavin.
    Differential outgrowth potential of Clostridium perfringens food-borne isolates with various cpe-genotypes in vacuum-packed ground beef during storage at 12°C
    Xiao, Y. ; Wagendorp, A. ; Abee, T. ; Wells-Bennik, M.H.J. - \ 2015
    International Journal of Food Microbiology 194 (2015). - ISSN 0168-1605 - p. 40 - 45.
    enterotoxin gene - multiplex pcr - heat-resistance - cooked beef - a strains - plasmid - growth - spores - sporulation - expression
    In the current study, the outgrowth of spores of 15 different food isolates of Clostridium perfringens was evaluated in vacuum-packed ground beef during storage at 12 °C and 25 °C. This included enterotoxic strains carrying the gene encoding the CPE enterotoxin on the chromosome (C-cpe), on a plasmid (P-cpe) and cpe-negative strains. The 15 strains were selected from a larger group of strains that were first evaluated for their ability to sporulate in modified Duncan–Strong sporulating medium. Sporulation ability varied greatly between strains but was not associated with a particular cpe genotype. In line with previous studies, the tested C-cpe strains produced spores with significantly higher heat resistance than the cpe-negative and P-cpe strains (both IS1151 and IS1470-like) with the exception of strain VWA009. Following inoculation of vacuum-packed cooked ground beef with spores, the heat-resistant C-cpe strains showed lower outgrowth potential in this model food stored at 12 °C than the P-cpe and cpe-negative strains, while no significant differences were observed at 25 °C. These results suggest that the latter strains may have a competitive advantage over C-cpe strains at reduced temperatures during storage of foods that support the growth of C. perfringens. While spores of P-cpe strains are readily inactivated by heat processing, post-processing contamination by food handlers who may carry P-cpe strains that have a better growth potential at lower temperatures must be avoided. The varying responses of C. perfringens spores to heat and the differences in outgrowth capacity at different temperatures are factors to be considered in strain selection for challenge tests, and for predictive modelling of C. perfringens.
    Network-based integration of molecular and physiological data elucidates regulatory mechanisms underlying adaptation to high-fat diet
    Derous, D. ; Kelder, T. ; Schothorst, E.M. van; Erk, M. van; Voigt, A. ; Klaus, S. ; Keijer, J. ; Radonjic, M. - \ 2015
    Genes & Nutrition 10 (2015)4. - ISSN 1555-8932
    obesity - disease - expression - receptor
    Health is influenced by interplay of molecular, physiological and environmental factors. To effectively maintain health and prevent disease, health-relevant relations need to be understood at multiple levels of biological complexity. Network-based methods provide a powerful platform for integration and mining of data and knowledge characterizing different aspects of health. Previously, we have reported physiological and gene expression changes associated with adaptation of murine epididymal white adipose tissue (eWAT) to 5 days and 12 weeks of high-fat diet (HFD) and low-fat diet feeding (Voigt et al. in Mol Nutr Food Res 57:1423–1434, 2013. doi:10.1002/mnfr.201200671). In the current study, we apply network analysis on this dataset to comprehensively characterize mechanisms driving the short- and long-term adaptation of eWAT to HFD across multiple levels of complexity. We built a three-layered interaction network comprising enriched biological processes, their transcriptional regulators and associated changes in physiological parameters. The multi-layered network model reveals that early eWAT adaptation to HFD feeding involves major changes at a molecular level, including activation of TGF-ß signalling pathway, immune and stress response and downregulation of mitochondrial functioning. Upon prolonged HFD intake, initial transcriptional response tails off, mitochondrial functioning is even further diminished, and in turn the relation between eWAT gene expression and physiological changes becomes more prominent. In particular, eWAT weight and total energy intake negatively correlate with cellular respiration process, revealing mitochondrial dysfunction as a hallmark of late eWAT adaptation to HFD. Apart from global understanding of the time-resolved adaptation to HFD, the multi-layered network model allows several novel mechanistic hypotheses to emerge: (1) early activation of TGF-ß signalling as a trigger for structural and morphological changes in mitochondrial organization in eWAT, (2) modulation of cellular respiration as an intervention strategy to effectively deal with excess dietary fat and (3) discovery of putative intervention targets, such those in pathways related to appetite control. In conclusion, the generated network model comprehensively characterizes eWAT adaptation to high-fat diet, spanning from global aspects to mechanistic details. Being open to further exploration by the research community, it provides a resource of health-relevant interactions ready to be used in a broad range of research applications.
    Reporters for sensitive and quantitative measurement of auxin response
    Liao, C.Y. ; Smet, W.M.S. ; Brunoud, G. ; Yoshida, S. ; Vernoux, T. ; Weijers, D. - \ 2015
    Nature Methods : techniques for life scientists and chemists 12 (2015). - ISSN 1548-7091 - p. 207 - 210.
    apical-basal axis - box protein tir1 - aux/iaa proteins - arabidopsis - transcription - expression - transport - specificity - sufficient - perception
    The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.
    The effects of environmental enrichment and age-related differences on inhibitory avoidance in zebrafish (Danio rerio Hamilton)
    Manuel, R. ; Gorissen, M. ; Stokkermans, M. ; Zethof, J. ; Ebbesson, L.O.E. ; Vis, J.W. van de; Flik, G. ; Bos, R. van den - \ 2015
    Zebrafish 12 (2015)2. - ISSN 1545-8547 - p. 152 - 165.
    corticotropin-releasing-factor - binding-protein - rearing environment - neurotrophic factor - emotional memory - factor crf - rat-brain - stress - fish - expression
    The inhibitory avoidance paradigm allows the study of mechanisms underlying learning and memory formation in zebrafish (Danio rerio Hamilton). For zebrafish, the physiology and behavior associated with this paradigm are as yet poorly understood. We therefore assessed the effects of environmental enrichment and fish age on inhibitory avoidance learning. Fish raised in an environmentally enriched tank showed decreased anxiety-like behavior and increased exploration. Enrichment greatly reduced inhibitory avoidance in 6-month (6M)- and 12-month (12M)-old fish. Following inhibitory avoidance, telencephalic mRNA levels of proliferating cell nuclear antigen (pcna), neurogenic differentiation (neurod), cocaine- and amphetamine-regulated transcript 4 (cart4), and cannabinoid receptor 1 (cnr1) were lower in enriched-housed fish, while the ratios of mineralocorticoid receptor (nr3c2)/glucocorticoid receptor a [nr3c1(a)] and glucocorticoid receptor ß [nr3c1(ß)]/glucocorticoid receptor a [nr3c1(a)] were higher. This was observed for 6M-old fish only, not for 24-month (24M) old fish. Instead, 24M-old fish showed delayed inhibitory avoidance, no effects of enrichment, and reduced expression of neuroplasticity genes. Overall, our data show strong differences in inhibitory avoidance behavior between zebrafish of different ages and a clear reduction in avoidance behavior following housing under environmental enrichment.
    Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon
    IJssennagger, N. ; Belzer, C. ; Hooiveld, G.J.E.J. ; Dekker, J. ; Mil, S.W.C. ; Müller, M.R. ; Kleerebezem, M. ; Meer, R. van der - \ 2015
    Proceedings of the National Academy of Sciences of the United States of America 112 (2015)32. - ISSN 0027-8424 - p. 10038 - 10043.
    colorectal-cancer - red meat - mice - mucin - fat - susceptibility - cytotoxicity - expression - inhibitor - bacterial
    Colorectal cancer risk is associated with diets high in red meat. Heme, the pigment of red meat, induces cytotoxicity of colonic contents and elicits epithelial damage and compensatory hyperproliferation, leading to hyperplasia. Here we explore the possible causal role of the gut microbiota in heme-induced hyperproliferation. To this end, mice were fed a purified control or heme diet (0.5 µmol/g heme) with or without broad-spectrum antibiotics for 14 d. Heme-induced hyperproliferation was shown to depend on the presence of the gut microbiota, because hyperproliferation was completely eliminated by antibiotics, although heme-induced luminal cytotoxicity was sustained in these mice. Colon mucosa transcriptomics revealed that antibiotics block heme-induced differential expression of oncogenes, tumor suppressors, and cell turnover genes, implying that antibiotic treatment prevented the heme-dependent cytotoxic micelles to reach the epithelium. Our results indicate that this occurs because antibiotics reinforce the mucus barrier by eliminating sulfide-producing bacteria and mucin-degrading bacteria (e.g., Akkermansia). Sulfide potently reduces disulfide bonds and can drive mucin denaturation and microbial access to the mucus layer. This reduction results in formation of trisulfides that can be detected in vitro and in vivo. Therefore, trisulfides can serve as a novel marker of colonic mucolysis and thus as a proxy for mucus barrier reduction. In feces, antibiotics drastically decreased trisulfides but increased mucin polymers that can be lysed by sulfide. We conclude that the gut microbiota is required for heme-induced epithelial hyperproliferation and hyperplasia because of the capacity to reduce mucus barrier function.
    Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Funtional Characterization of the Three First Steps of the Pathway in Slavia Fruicosa and Rosmarinus officinalis
    Bozic, D. ; Papaefthimiou, D. ; Brückner, K. ; Vos, C.H.R. de; Tsoleridis, C.A. ; Katsarou, D. ; Papanikolaou, A. ; Pateraki, I. ; Chatzopoulou, F.M. ; Dimitriadou, E. ; Kostas, S. ; Manzano, D. ; Scheler, U. ; Ferrer, A. ; Tissier, A. ; Makris, A.M. ; Kampranis, S.C. ; Kanellis, A. - \ 2015
    PLoS ONE 10 (2015)5. - ISSN 1932-6203 - 28 p.
    creticus subsp creticus - in-vitro antioxidant - diphosphate synthase - subcellular-localization - phenolic diterpenes - gene-cluster - rosemary - l. - expression - metabolism
    Carnosic acid (CA) is a phenolic diterpene with anti-tumour, anti-diabetic, antibacterial and neuroprotective properties that is produced by a number of species from several genera of the Lamiaceae family, including Salvia fruticosa (Cretan sage) and Rosmarinus officinalis (Rosemary). To elucidate CA biosynthesis, glandular trichome transcriptome data of S. fruticosa were mined for terpene synthase genes. Two putative diterpene synthase genes, namely SfCPSand SfKSL, showing similarities to copalyl diphosphate synthase and kaurene synthase-like genes, respectively, were isolated and functionally characterized. Recombinant expression in Escherichia coli followed by in vitro enzyme activity assays confirmed that SfCPS is a copalyl diphosphate synthase. Coupling of SfCPS with SfKSL,both in vitro and in yeast, resulted in the synthesis miltiradiene, as confirmed by 1D and 2D NMR analyses (1H, 13C, DEPT, COSY H-H, HMQC and HMBC). Coupled transient in vivo assays of SfCPS and SfKSL in Nicotiana benthamiana further confirmed production of miltiradiene in planta. To elucidate the subsequent biosynthetic step, RNA-Seq data of S.fruticosa and R. officinalis were searched for cytochrome P450 (CYP) encoding genes potentially involved in the synthesis of the first phenolic compound in the CA pathway, ferruginol. Three candidate genes were selected, SfFS, RoFS1 and RoFS2. Using yeast and N. benthamiana expression systems, all three where confirmed to be coding for ferruginol synthases, thus revealing the enzymatic activities responsible for the first three steps leading to CA in two Lamiaceae genera.
    The butterfly plant arms-race escalated by gene and genome duplications
    Edger, P.P. ; Heidel-Fischer, H.M. ; Bekaert, K.M. ; Rota, J. ; Glockner, G. ; Platts, A.E. ; Heckel, D.G. ; Der, J.P. ; Wafula, E.K. ; Tang, M. ; Hofberger, J.A. ; Smithson, A. ; Hall, J.C. ; Blanchette, M. ; Bureau, T.E. ; Wright, S.I. ; dePamphilis, C.W. ; Schranz, M.E. ; Conant, G.C. ; Barker, M.S. ; Wahlberg, N. ; Vogel, H. ; Pires, J.C. ; Wheat, C.W. - \ 2015
    Proceedings of the National Academy of Sciences of the United States of America 112 (2015)27. - ISSN 0027-8424 - p. 8362 - 8366.
    evolutionaire genetica - co-evolutie - diversificatie - brassica - pieridae - papilionidae - glucosinolaten - fylogenie - evolutionary genetics - coevolution - diversification - brassica - pieridae - papilionidae - glucosinolates - phylogeny - diversity - defense - cytochrome-p450 - polymorphism - arabidopsis - metabolism - expression - speciation
    Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.
    Drought stress affects plant metabolites and herbivore preference but not host location by its parasitoids
    Weldegergis, B.T. ; Zhu, F. ; Poelman, E.H. ; Dicke, M. - \ 2015
    Oecologia 177 (2015)3. - ISSN 0029-8549 - p. 701 - 713.
    volatile emissions - water-stress - abiotic factors - oviposition - genes - biosynthesis - consequences - lepidoptera - complexity - expression
    One of the main abiotic stresses that strongly affects plant survival and the primary cause of crop loss around the world is drought. Drought stress leads to sequential morphological, physiological, biochemical and molecular changes that can have severe effects on plant growth, development and productivity. As a consequence of these changes, the interaction between plants and insects can be altered. Using cultivated Brassica oleracea plants, the parasitoid Microplitis mediator and its herbivorous host Mamestra brassicae, we studied the effect of drought stress on (1) the emission of plant volatile organic compounds (VOCs), (2) plant hormone titres, (3) preference and performance of the herbivore, and (4) preference of the parasitoid. Higher levels of jasmonic acid (JA) and abscisic acid (ABA) were recorded in response to herbivory, but no significant differences were observed for salicylic acid (SA) and indole-3-acetic acid (IAA). Drought significantly impacted SA level and showed a significant interactive effect with herbivory for IAA levels. A total of 55 VOCs were recorded and the difference among the treatments was influenced largely by herbivory, where the emission rate of fatty acid-derived volatiles, nitriles and (E)-4,8-dimethylnona-1,3,7-triene [(E)-DMNT] was enhanced. Mamestra brassicae moths preferred to lay eggs on drought-stressed over control plants; their offspring performed similarly on plants of both treatments. VOCs due to drought did not affect the choice of M. mediator parasitoids. Overall, our study reveals an influence of drought on plant chemistry and insect-plant interactions.
    An acute intake of plant stanol esters alters immune-related pathways in the jejunum of healthy volunteers
    Smet, E. de; Mensink, M.R. ; Boekschoten, M.V. ; Ridder, R. de; Germeraad, W.T.V. ; Wolfs, T.G.A.M. ; Plat, J. - \ 2015
    The British journal of nutrition 113 (2015)5. - ISSN 0007-1145 - p. 794 - 802.
    atp-binding cassette - triglyceride transfer protein - niemann-pick c1-like-1 - cholesterol-metabolism - dietary phytosterols - beta-sitosterol - sterol-metabolism - messenger-rna - expression - abcg8
    Plant sterols and stanols inhibit intestinal cholesterol absorption and consequently lower serum LDL-cholesterol (LDL-C) concentrations. The underlying mechanisms are not yet known. In vitro and animal studies have suggested that changes in intestinal sterol metabolism are attributed to the LDL-C-lowering effects of plant stanol esters. However, similar studies in human subjects are lacking. Therefore, we examined the effects of an acute intake of plant stanol esters on gene expression profiles of the upper small intestine in healthy volunteers. In a double-blind cross-over design, fourteen healthy subjects (eight female and six male; age 21–55 years), with a BMI ranging from 21 to 29 kg/m2, received in random order a shake with or without plant stanol esters (4 g). At 5 h after consumption of the shake, biopsies were taken from the duodenum (around the papilla of Vater) and from the jejunum (20 cm distal from the papilla of Vater). Microarray analysis showed that the expression profiles of genes involved in sterol metabolism were not altered. Surprisingly, the pathways involved in T-cell functions were down-regulated in the jejunum. Furthermore, immunohistochemical analysis showed that the number of CD3 (cluster of differentiation number 3), CD4 (cluster of differentiation number 4) and Foxp3+ (forkhead box P3-positive) cells was reduced in the plant stanol ester condition compared with the control condition, which is in line with the microarray data. The physiological and functional consequences of the plant stanol ester-induced reduction of intestinal T-cell-based immune activity in healthy subjects deserve further investigation.
    p21 Ablation in Liver Enhances DNA Damage, Cholestasis, and Carcinogenesis
    Ehedego, H. ; Boekschoten, M.V. ; Hu, W. ; Doler, C. ; Haybaeck, J. ; Gassler, N. ; Muller, M.R. ; Liedtke, C. ; Trautwein, C. - \ 2015
    Cancer Research 75 (2015)6. - ISSN 0008-5472 - p. 1144 - 1155.
    kinase inhibitor p21 - human hepatocellular-carcinoma - cell-cycle progression - rad51 overexpression - expression - p21(waf1/cip1) - mice - inflammation - regeneration - repair
    Genetic mouse studies suggest that the NF-¿B pathway regulator NEMO (also known as IKK¿) controls chronic inflammation and carcinogenesis in the liver. However, the molecular mechanisms explaining the function of NEMO are not well defined. Here, we report that overexpression of the cell-cycle regulator p21 is a critical feature of liver inflammation and carcinogenesis caused by the loss of NEMO. NEMO¿hepa mice develop chronic hepatitis characterized by increased hepatocyte apoptosis and proliferation that causes the development of fibrosis and hepatocellular carcinoma (HCC), similar to the situation in human liver disease. Having identified p21 overexpression in this model, we evaluated its role in disease progression and LPS-mediated liver injury in double mutant NEMO¿hepa/p21-/- mice. Eight-week-old NEMO¿hepa/p21-/- animals displayed accelerated liver damage that was not associated with alterations in cell-cycle progression or the inflammatory response. However, livers from NEMO¿hepa/p21-/- mice displayed more severe DNA damage that was further characterized by LPS administration correlating with higher lethality of the animals. This phenotype was attenuated by genetic ablation of the TNF receptor TNF-R1 in NEMO¿hepa/p21-/- mice, demonstrating that DNA damage is induced via TNF. One-year-old NEMO¿hepa/p21-/- mice displayed greater numbers of HCC and severe cholestasis compared with NEMO¿hepa animals. Therefore, p21 overexpression in NEMO¿hepa animals protects against DNA damage, acceleration of hepatocarcinogenesis, and cholestasis. Taken together, our findings illustrate how loss of NEMO promotes chronic liver inflammation and carcinogenesis, and they identify a novel protective role for p21 against the generation of DNA damage.
    Cisgenic apple trees; development, characterization, and performance
    Krens, F.A. ; Schaart, J.G. ; Burgh, A.M. van der; Tinnenbroek-Capel, I.E.M. ; Groenwold, R. ; Kodde, L.P. ; Broggini, G.A.L. ; Gessler, C. ; Schouten, H.J. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 11 p.
    scab resistance gene - selectable marker - mediated transformation - plant transformation - transcription factor - transgenic apple - agrobacterium - gala - recombinase - expression
    Two methods were developed for the generation of cisgenic apples. Both have been successfully applied producing trees. The first method avoids the use of any foreign selectable marker genes; only the gene-of-interest is integrated between the T-DNA border sequences. The second method makes use of recombinase-based marker excision. For the first method we used the MdMYB10 gene from a red-fleshed apple coding for a transcription factor involved in regulating anthocyanin biosynthesis. Red plantlets were obtained and presence of the cisgene was confirmed. Plantlets were grafted and grown in a greenhouse. After 3 years, the first flowers appeared, showing red petals. Pollination led to production of red-fleshed cisgenic apples. The second method used the pM(arker)F(ree) vector system, introducing the scab resistance gene Rvi6, derived from apple. Agrobacterium-mediated transformation, followed by selection on kanamycin, produced genetically modified apple lines. Next, leaves from in vitro material were treated to activate the recombinase leading to excision of selection genes. Subsequently, the leaf explants were subjected to negative selection for marker-free plantlets by inducing regeneration on medium containing 5-fluorocytosine. After verification of the marker-free nature, the obtained plants were grafted onto rootstocks. Young trees from four cisgenic lines and one intragenic line, all containing Rvi6, were planted in an orchard. Appropriate controls were incorporated in this trial. We scored scab incidence for three consecutive years on leaves after inoculations with Rvi6-avirulent strains. One cisgenic line and the intragenic line performed as well as the resistant control. In 2014 trees started to overcome their juvenile character and formed flowers and fruits. The first results of scoring scab symptoms on apple fruits were obtained. Apple fruits from susceptible controls showed scab symptoms, while fruits from cisgenic and intragenic lines were free of scab.
    Deconjugation of soy isoflavone glucuronides needed for estrogenic activity
    Islam, M.A. ; Bekele, R. ; Berg, J.H.J. van den; Kuswanti, Y. ; Thapa, O. ; Soltani, S. ; Leeuwen, F.X.R. ; Rietjens, I.M.C.M. ; Murk, A.J. - \ 2015
    Toxicology in Vitro 29 (2015)4. - ISSN 0887-2333 - p. 706 - 715.
    beta-messenger-rna - in-vitro - er-beta - receptor-beta - cell-proliferation - human plasma - cancer - expression - alpha - genistein
    Soy isoflavones (SIF) are present in the systemic circulation as conjugated forms of which the estrogenic potency is not yet clear. The present study provides evidence that the major SIF glucuronide metabolites in blood, genistein-7-O-glucuronide (GG) and daidzein-7-O-glucuronide (DG), only become estrogenic after deconjugation. The estrogenic potencies of genistein (Ge), daidzein (Da), GG and DG were determined using stably transfected U2OS-ERa, U2OS-ERß reporter gene cells and proliferation was tested in T47D-ERß cells mimicking the ERa/ERß ratio of healthy breast cells and inT47D breast cancer cells. In all assays applied, the estrogenic potency of the aglycones was significantly higher than that of their corresponding glucuronides. UPLC analysis revealed that in U2OS and T47D cells, 0.2-1.6% of the glucuronides were deconjugated to their corresponding aglycones. The resulting aglycone concentrations can account for the estrogenicity observed upon glucuronide exposure. Interestingly, under similar experimental conditions, rat breast tissue S9 fraction was about 30 times more potent in deconjugating these glucuronides than human breast tissue S9 fraction. Our study confirms that SIF glucuronides are not estrogenic as such, and that the small % of deconjugation in the cell is enough to explain the slight bioactivity observed for the SIF-glucuronides. Species differences in deconjugation capacity should be taken into account when basing risk-benefit assessment of these SIF for the human population on animal data.
    Mutrivariate and univariate analysis of energy balance data from lactating dairy cows
    Moraes, L.E. ; Kebreab, E. ; Strathe, A.B. ; Dijkstra, J. ; France, J. ; Casper, D.P. ; Fadel, J.G. - \ 2015
    Journal of Dairy Science 98 (2015)6. - ISSN 0022-0302 - p. 4012 - 4029.
    body tissue mobilization - random regression - equation models - milk-production - major advances - genetic merit - growing pigs - net energy - efficiency - expression
    The objectives of the study were to develop a multivariate framework for analyzing energy balance data from lactating cows and investigate potential changes in maintenance requirements and partial efficiencies of energy utilization by lactating cows over the years. The proposed model accounted for the fact that metabolizable energy intake, milk energy output, and tissue energy balance are random variables that interact mutually. The model was specified through structural equations implemented in a Bayesian framework. The structural equations, along with a model traditionally used to estimate energetic parameters, were fitted to a large database of indirect calorimetry records from lactating cows. Maintenance requirements and partial efficiencies for both models were similar to values reported in the literature. In particular, the estimated parameters (with 95% credible interval in parentheses) for the proposed model were: net energy requirement for maintenance equal to 0.36 (0.34, 0.38) MJ/kg of metabolic body weight·day; the efficiency of utilizing dietary energy for milk production and tissue gain were 0.63 (0.61, 0.64) and 0.70 (0.68, 0.72), respectively; the efficiency of utilizing body stores for milk production was 0.89 (0.87, 0.91). Furthermore, additional analyses were conducted for which energetic parameters were allowed to depend on the decade in which studies were conducted. These models investigated potential changes in maintenance requirements and partial efficiencies over the years. Canonical correlation analysis was used to investigate the association between changes in energetic parameters with additional dietary and animal characteristics available in the database. For both models, net energy requirement for maintenance and the efficiency of utilizing dietary energy for milk production and tissue gain increased in the more recent decades, whereas the efficiency of utilizing body stores for milk production remained unchanged. The increase in maintenance requirements in modern milk production systems is consistent with the literature that describes increased fasting heat production in cows of higher genetic merit. The increase in utilization of dietary energy for milk production and tissue gain was partially attributed to the changes in dietary composition, in particular to the increase in dietary ether extract to levels closer to currently observed in modern milk production systems. Therefore, the estimated energetic parameters from this study can be used to update maintenance requirements and partial efficiencies of energy utilization in North American feeding systems for lactating cows.
    Long-lasting effects of Early-life Antibiotic Treatment and routine Animal Handling on Gut Microbiota Composition and Immune System in Pigs
    Schokker, D. ; Zhang, J. ; Vastenhouw, S.A. ; Heilig, G.H.J. ; Smidt, H. ; Rebel, J.M.J. ; Smits, M.A. - \ 2015
    PLoS ONE 10 (2015)2. - ISSN 1932-6203
    large gene lists - intestinal microbiota - bacterial - extraction - expression - disease - health - asthma - young - diet
    Background In intensive pig husbandry systems, antibiotics are frequently administrated during early life stages to prevent respiratory and gastro-intestinal tract infections, often in combination with stressful handlings. The immediate effects of these treatments on microbial colonization and immune development have been described recently. Here we studied whether the early life administration of antibiotics has long-lasting effects on the pig’s intestinal microbial community and on gut functionality. Methodology/Principal Findings To investigate the long-lasting effect of early-life treatment, piglets were divided into three different groups receiving the following treatments: 1) no antibiotics and no stress, 2) antibiotics and no stress, and 3) antibiotics and stress. All treatments were applied at day four after birth. Sampling of jejunal content for community scale microbiota analysis, and jejunal and ileal tissue for genome-wide transcription profiling, was performed at day 55 (~8 weeks) and day 176 (~25 weeks) after birth. Antibiotic treatment in combination with or without exposure to stress was found to have long-lasting effects on host intestinal gene expression involved in a multitude of processes, including immune related processes. Conclusions/Significance The results obtained in this study indicate that early life (day 4 after birth) perturbations have long-lasting effects on the gut system, both in gene expression (day 55) as well as on microbiota composition (day 176). At day 55 high variance was observed in the microbiota data, but no significant differences between treatment groups, which is most probably due to the newly acquired microbiota during and right after weaning (day 28). Based on the observed difference in gene expression at day 55, it is hypothesized that due to the difference in immune programming during early life, the systems respond differently to the post-weaning newly acquired microbiota. As a consequence, the gut systems of the treatment groups develop into different homeostasis.
    Impact of a novel protein meal on the gastrointesinal microbiota and host transciptome of larval zebrafish Danio rerio
    Rurangwa, E. ; Sipkema, D. ; Kals, J. ; Veld, M. ter; Forlenza, M. ; Bacanu, G.M. ; Smidt, H. ; Palstra, A.P. - \ 2015
    Frontiers in Physiology 6 (2015). - ISSN 1664-042X - 27 p.
    large gene lists - intestinal microbiota - gut microbiota - digestive physiology - solea-senegalensis - metal uptake - sp-nov - fish - expression - iron
    Larval zebrafish was subjected to a methodological exploration of the gastrointestinal microbiota and transcriptome. Assessed was the impact of two dietary inclusion levels of a novel protein meal (NPM) of animal origin (ragworm Nereis virens) on the gastrointestinal tract (GIT). Microbial development was assessed over the first 21 days post egg fertilisation (dpf) through 16S rRNA gene-based microbial composition profiling by pyrosequencing. Differentially expressed genes in the GIT were demonstrated at 21 dpf by whole transcriptome sequencing (mRNAseq). Larval zebrafish showed rapid temporal changes in microbial colonization but domination occurred by one to three bacterial species generally belonging to Proteobacteria and Firmicutes. The high iron content of NPM may have led to an increased relative abundance of bacteria that were related to potential pathogens and bacteria with an increased iron metabolism. Functional classification of the 328 differentially expressed genes indicated that the GIT of larvae fed at higher NPM level was more active in transmembrane ion transport and protein synthesis. mRNAseq analysis did not reveal a major activation of genes involved in the immune response or indicating differences in iron uptake and homeostasis in zebrafish fed at the high inclusion level of NPM
    A Quantitative and Dynamic Model of the Arabidopsis Flowering Time Gene Regulatory Network
    Valentim, F.L. ; Mourik, S. van; Posé, D. ; Kim, M.C. ; Schmid, M. ; Ham, R.C.H.J. van; Busscher, M. ; Sanchez Perez, G.F. ; Molenaar, J. ; Angenent, G.C. ; Immink, R.G.H. ; Dijk, A.D.J. van - \ 2015
    PLoS ONE 10 (2015)2. - ISSN 1932-6203
    floral transition - feedback loops - ft protein - expression - induction - transport - thaliana - signals - leafy - soc1
    Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.
    A complex interplay of tandem- and whole genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae
    Hofberger, J.A. ; Nsibo, D.L. ; Govers, F. ; Bouwmeester, K. ; Schranz, M.E. - \ 2015
    Genome Biology and Evolution 7 (2015)3. - ISSN 1759-6653 - p. 720 - 734.
    disease resistance genes - arabidopsis-thaliana - phylogenetic analysis - triggered immunity - provides insight - wide analysis - evolution - plants - diversification - expression
    The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding.
    The cell size distribution of tomato fruit can be changed by overexpression of CDKA1
    Czerednik, A. ; Busscher, M. ; Angenent, G.C. ; Maagd, R.A. de - \ 2015
    Plant Biotechnology Journal 13 (2015)2. - ISSN 1467-7644 - p. 259 - 268.
    cyclin-dependent kinase - lycopersicon-esculentum mill - plant development - arabidopsis - endoreduplication - growth - gene - expression - division - dna
    Tomato is one of the most cultivated vegetables in the world and an important ingredient of the human diet. Tomato breeders and growers face a continuous challenge of combining high quantity (production volume) with high quality (appearance, taste and perception for the consumers, processing quality for the processing industry). To improve the quality of tomato, it is important to understand the regulation of fruit development and of fruit cellular structure, which is in part determined by the sizes and numbers of cells within a tissue. The role of the cell cycle therein is poorly understood. Plant cyclin-dependent kinases (CDKs) are homologues of yeast cdc2, an important cell cycle regulator conserved throughout all eukaryotes. CDKA1 is constitutively expressed during the cell cycle and has dual functions in S- and M-phase progression. We have produced transgenic tomato plants with increased expression of CDKA1 under the control of the fruit-specific TPRP promoter, which despite a reduced number of seeds and diminished amount of jelly, developed fruits with weight and shape comparable to that of wild-type fruits. However, the phenotypic changes with regard to the pericarp thickness and placenta area were remarkable. Fruits of tomato plants with the highest expression of CDKA1 had larger septa and columella (placenta), compared with wild-type fruits. Our data demonstrate the possibility of manipulating the ratio between cell division and expansion by changing the expression of a key cell cycle regulator and probably its activity with substantial effects on structural traits of the harvested fruit.
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