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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    BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
    Katayama, T. ; Wilkinson, M.D. ; Aoki-Kinoshita, K.F. ; Prins, J.C.P. - \ 2014
    Journal of Biomedical Semantics 5 (2014). - ISSN 2041-1480
    genome analysis environment - metabolic pathways - web services - gene - sequences - software - biology - normalization - collection - glycomics
    The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
    A weighted AMMI Algorithm to Study Genotype-by-Environment Interaction and QTL-by-Environment Interaction
    Rodrigues, P.C. ; Malosetti, M. ; Gauch, H.G. - \ 2014
    Crop Science 54 (2014)4. - ISSN 0011-183X - p. 1555 - 1570.
    principal component analysis - multiplicative interaction-model - joint regression-analysis - additive main - cross-validation - yield trials - barley cross - mixed-model - selection - gene
    Genotype-by-environment (G × E) interaction (GEI) and quantitative trait locus (QTL)-by-environment interaction (QEI) are common phenomena in multiple-environment trials and represent a major challenge to breeders. The additive main effects and multiplicative interaction (AMMI) model is a widely used tool for the analysis of multiple-environment trials, where the data are represented by a two-way table of G × E means. For complete tables, least squares estimation for the AMMI model is equivalent to fitting an additive two-way ANOVA model for the main effects and applying a singular value decomposition to the interaction residuals, thereby implicitly assuming equal weights for all G × E means. However, multiple-environment data with strong GEI are often also characterized by strong heterogeneous error variation. To improve the performance of the AMMI model in the latter situation, we introduce a generalized estimation scheme, the weighted AMMI or W-AMMI algorithm. This algorithm is useful for studying GEI and QEI. For QEI, the W-AMMI algorithm can be used to create predicted values per environment that are subjected to QTL analysis. We compare the performance of this combined W-AMMI and QTL mapping strategy to direct QTL mapping on G × E means and to QTL mapping on AMMI-predicted values, again with QTL analyses for individual environments. Finally, we compare the W-AMMI QTL mapping strategy, with a multi-environment mixed model QTL mapping approach. Two data sets are used: (i) data from a simulated pepper (Capsicum annuum L.) back cross population using a crop growth model to relate genotypes to phenotypes in a nonlinear way, and (ii) the doubled-haploid Steptoe × Morex barley (Hordeum vulgare L.) population. The QTL analyses on the W-AMMI-predicted values outperformed the QTL analyses on the G × E means and on the AMMI-predicted values, and were very similar to the mixed model QTL mapping approach with regard to the number and location of the true positive QTLs detected, especially for QTLs associated with the interaction and for environments with higher error variance. W-AMMI analysis for GEI and QEI provides an easy-to-use and robust tool with wide applicability.
    Adipose tissue metabolism and inflammation are differently affected by weight loss in obese mice due to either a high-fat diet restriction or change to a low-fat diet
    Hoevenaars, F.P.M. ; Keijer, J. ; Herreman, L. ; Palm, I.F. ; Hegeman, M.A. ; Swarts, J.J.M. ; Schothorst, E.M. van - \ 2014
    Genes & Nutrition 9 (2014). - ISSN 1555-8932 - 11 p.
    nicotinamide nucleotide transhydrogenase - c57bl/6j mice - mitochondrial biogenesis - energy restriction - insulin-resistance - glucose - acid - expression - health - gene
    Restriction of a high-fat diet (HFD) and a change to a low-fat diet (LFD) are two interventions that were shown to promote weight loss and improve parameters of metabolic health in obesity. Examination of the biochemical and molecular responses of white adipose tissue (WAT) to these interventions has not been performed so far. Here, male C57BL/6JOlaHsd mice, harboring an intact nicotinamide nucleotide transhydrogenase gene, were fed a purified 40 energy% HFD for 14 weeks to induce obesity. Afterward, mice were divided into three dietary groups: HFD (maintained on HFD), LFD (changed to LFD with identical ingredients), and HFD-CR (restricted to 70 % of the HFD). The effects of the interventions were examined after 5 weeks. Beneficial effects were seen for both HFD-CR and LFD (compared to HFD) regarding physiological parameters (body weight and fat mass) and metabolic parameters, including circulating insulin and leptin levels. Macrophage infiltration in WAT was reduced by both interventions, although more effectively by HFDCR. Strikingly, molecular parameters in WAT differed between HFD-CR and LFD, with increased activation of mitochondrial carbohydrate and fat metabolism in HFDCR mice. Our results confirm that restriction of the amount of dietary intake and reduction in the dietary energy content are both effective in inducing weight loss. The larger decrease in WAT inflammation and increase in mitochondrial carbohydrate metabolism may be due to a larger degree of energy restriction in HFD-CR, but could also be due to superior effectiveness of dietary restriction in weight loss strategies.
    Analysis of the A-U rich hairpin from the intergenic region of tospovirus S RNA as target and inducer of RNA silencing
    Hedil, M. ; Hassani-Mehraban, A. ; Lohuis, D. ; Kormelink, R.J.M. - \ 2014
    PLoS ONE 9 (2014)9. - ISSN 1932-6203 - 10 p.
    spotted-wilt-virus - small interfering rnas - double-stranded-rna - viral suppressors - gene - protein - plants - sequence - arabidopsis - resistance
    Earlier work indicated that Tomato spotted wilt virus (TSWV) messenger transcripts, and not the (anti)genomic RNAs, are targeted by the RNA silencing machinery. Here, the predicted AU-rich hairpin (HP) structure encoded by the intergenic region (IGR) of the TSWV S RNA, and present at the 3' end of viral mRNAs, was analyzed as a target and inducer for RNA silencing. Virus-derived siRNAs (vsiRNAs) purified from virus infected plants were found to derive from all three genomic RNA segments but predominantly the ambisense M and S RNAs. Further profiling on the S RNA sequence revealed that vsiRNAs were found from almost the entire S RNA sequence, except the IGR from where hardly any vsiRNAs were found. Similar profiles were observed with the distantly related Tomato yellow ring tospovirus (TYRV). Dicer cleavage assays using Drosophila melanogaster (Dm) embryo extracts showed that synthetic transcripts of the IGR-HP region were recognized as substrate for Dicer. Transient agroinfiltration assays of a GFP-sensor construct containing the IGR-HP sequence at its 3' UTR (GFP-HP) did not show more rapid/strong silencing and profiling of the corresponding siRNAs, generated outside the context of a viral infection, still revealed relatively low levels of IGR-HP-derived siRNAs. These data support the idea that the IGR-HP is a weak inducer of RNA silencing and only plays a minor role in the amplification of a strong antiviral RNAi response.
    Phenotypic analyses of Arabidopsis T-DNA insertion lines and expression profiling reveal that multiple L-type lectin receptor kinases are involved in plant immunity
    Wang, Y. ; Bouwmeester, K. ; Beseh, P. ; Shan, W. ; Govers, F. - \ 2014
    Molecular Plant-Microbe Interactions 27 (2014)12. - ISSN 0894-0282 - p. 1390 - 1402.
    pattern-triggered immunity - phytophthora-infestans - salicylic-acid - defense responses - innate immunity - thaliana - gene - resistance - biology - roles
    L-type lectin receptor kinases (LecRKs) are membrane-spanning receptor-like kinases with putative roles in biotic and abiotic stress responses and in plant development. In Arabidopsis, 45 LecRKs were identified but their functions are largely unknown. Here, a systematic functional analysis was carried out by evaluating phenotypic changes of Arabidopsis LecRK T-DNA insertion lines in plant development and upon exposure to various external stimuli. None of the LecRK T-DNA insertion lines showed clear developmental changes, neither under normal conditions nor upon abiotic stress treatment. However, many of the T-DNA insertion lines showed altered resistance to Phytophthora brassicae, Phytophthora capsici, Pseudomonas syringae or Alternaria brassicicola. One mutant defective in LecRK-V.5 expression, was compromised in resistance to two Phytophthora spp. but showed enhanced resistance to P. syringae. LecRK-V.5 overexpression confirmed its dual role in resistance and susceptibility depending on the pathogen. Combined analysis of these phenotypic data and LecRK expression profiles retrieved from public datasets revealed that LecRKs which are hardly induced upon infection or even suppressed are also involved in pathogen resistance. Computed co-expression analysis revealed that LecRKs with similar function displayed diverse expression patterns. Since LecRKs are widespread in plants, the results presented here provide invaluable information for exploring the potential of LecRKs as novel sources of resistance in crops.
    A strategy for developing representative germplasm sets for systematic QTL validation, demonstrated for apple, peach, and sweet cherry
    Peace, C.P. ; Luby, J. ; Weg, W.E. van de; Bink, M.C.A.M. ; Iezzoni, A.F. - \ 2014
    Tree Genetics and Genomes 10 (2014)6. - ISSN 1614-2942 - p. 1679 - 1694.
    x domestica borkh. - marker-assisted selection - fire blight resistance - breeding program - population-structure - pyrus-communis - fruit firmness - map position - md-acs1 - gene
    Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were developed in the marker-assisted breeding (MAB)-enabling “RosBREED” project as a base resource for QTL validation in US breeding germplasm of apple (Malus × domestica), peach (Prunus persica), and sweet cherry (Prunus avium) consisting of 467, 452, and 268 individuals, respectively. These sets adequately represent the most designated IBPs, have distinct advantages for QTL validation over other germplasm arrangements of equal size, and are recommended as a base resource for QTL validation by breeders of these US crops. The strategy described here can be used to develop efficient reference germplasm sets suiting other breeding genepools or to calculate the statistical power for QTL validation of germplasm sets already established.
    Circulation of four Anaplasma phagocytophilum ecotypes in Europe
    Jahfari, S. ; Coipan, E.C. ; Fonville, M. ; Leeuwen, A.D. van; Hengeveld, P. ; Heylen, D. ; Heyman, P. ; Maanen, C. van; Butler, C.M. ; Foldvari, G. ; Szekeres, S. ; Duijvendijk, L.A.G. van; Tack, W. ; Rijks, J.M. ; Giessen, J. van der; Takken, W. ; Wieren, S.E. van; Takumi, K. ; Sprong, H. - \ 2014
    Parasites & Vectors 7 (2014)1. - ISSN 1756-3305
    candidatus neoehrlichia mikurensis - human granulocytic anaplasmosis - ixodes-ricinus ticks - borrelia-burgdorferi - borne diseases - phylogenetic analyses - sequence-analysis - ehrlichiosis - strains - gene
    Background: Anaplasma phagocytophilum is the etiological agent of granulocytic anaplasmosis in humans and animals. Wild animals and ticks play key roles in the enzootic cycles of the pathogen. Potential ecotypes of A. phagocytophilum have been characterized genetically, but their host range, zoonotic potential and transmission dynamics has only incompletely been resolved. Methods. The presence of A. phagocytophilum DNA was determined in more than 6000 ixodid ticks collected from the vegetation and wildlife, in 289 tissue samples from wild and domestic animals, and 69 keds collected from deer, originating from various geographic locations in The Netherlands and Belgium. From the qPCR-positive lysates, a fragment of the groEL-gene was amplified and sequenced. Additional groEL sequences from ticks and animals from Europe were obtained from GenBank, and sequences from human cases were obtained through literature searches. Statistical analyses were performed to identify A. phagocytophilum ecotypes, to assess their host range and their zoonotic potential. The population dynamics of A. phagocytophilum ecotypes was investigated using population genetic analyses. Results: DNA of A. phagocytophilum was present in all stages of questing and feeding Ixodes ricinus, feeding I. hexagonus, I. frontalis, I. trianguliceps, and deer keds, but was absent in questing I. arboricola and Dermacentor reticulatus. DNA of A. phagocytophilum was present in feeding ticks and tissues from many vertebrates, including roe deer, mouflon, red foxes, wild boar, sheep and hedgehogs but was rarely found in rodents and birds and was absent in badgers and lizards. Four geographically dispersed A. phagocytophilum ecotypes were identified, that had significantly different host ranges. All sequences from human cases belonged to only one of these ecotypes. Based on population genetic parameters, the potentially zoonotic ecotype showed significant expansion. Conclusion: Four ecotypes of A. phagocytophilum with differential enzootic cycles were identified. So far, all human cases clustered in only one of these ecotypes. The zoonotic ecotype has the broadest range of wildlife hosts. The expansion of the zoonotic A. phagocytophilum ecotype indicates a recent increase of the acarological risk of exposure of humans and animals.
    Soybean SAT1 (Symbiotic Ammonium Transporter 1) encodes a bHLH transcription factor involved in nodule growth and NH4+ transport
    Chiasson, D.M. ; Loughlin, P.C. ; Mazurkiewicz, D. ; Mohammadidehcheshmeh, M. ; Fedorova, E.E. ; Okamoto, M. ; McLean, E. ; Glass, A.D.M. ; Smith, S.E. ; Bisseling, T. ; Tyerman, S.D. ; Day, D.A. ; Kaiser, B.N. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)13. - ISSN 0027-8424 - p. 4814 - 4819.
    arabidopsis-thaliana - circadian clock - lotus-japonicus - stress-response - er stress - membrane - protein - expression - domain - gene
    Glycine max symbiotic ammonium transporter 1 was first documented as a putative ammonium (NH4+) channel localized to the symbiosome membrane of soybean root nodules. We show that Glycine max symbiotic ammonium transporter 1 is actually a membrane-localized basic helix–loop–helix (bHLH) DNA-binding transcription factor now renamed Glycine max bHLH membrane 1 (GmbHLHm1). In yeast, GmbHLHm1 enters the nucleus and transcriptionally activates a unique plasma membrane NH4+ channel Saccharomyces cerevisiae ammonium facilitator 1. Ammonium facilitator 1 homologs are present in soybean and other plant species, where they often share chromosomal microsynteny with bHLHm1 loci. GmbHLHm1 is important to the soybean rhizobium symbiosis because loss of activity results in a reduction of nodule fitness and growth. Transcriptional changes in nodules highlight downstream signaling pathways involving circadian clock regulation, nutrient transport, hormone signaling, and cell wall modification. Collectively, these results show that GmbHLHm1 influences nodule development and activity and is linked to a novel mechanism for NH4+ transport common to both yeast and plants.
    Regeneration and transformation of Crambe abyssinica
    Qi, W. ; Tinnenbroek-Capel, I.E.M. ; Schaart, J. ; Huang Bangquan, ; Cheng, J. ; Visser, R.G.F. ; Loo, E.N. van; Krens, F.A. - \ 2014
    BMC Plant Biology 14 (2014). - ISSN 1471-2229 - 12 p.
    gene - agrobacterium - tissue - plants
    Background: Crambe abyssinica (crambe) is a non-food oil seed crop. Its seed oil is widely used in the chemical industry because of the high erucic acid content. Furthermore, it is a potential platform for various feedstock oils for industrial uses based on genetic modification. Here, we describe the development of a series of protocols for all steps required in the process of generating genetically modified crambe. Results: Different explant types from crambe seedlings were tested for shoot regeneration using different hormone-combinations. Cotyledonary nodes on basic medium with 0.5 µM NAA and 2.2 µM BAP gave the highest regeneration percentages. For propagation by tissue culture, explants of stems, petioles, leaves and axillary buds of in vitro plantlets were tested using the optimized medium. Axillary buds showed the highest shoot proliferation efficiency. Cotyledonary nodes were used to test the proper concentration of kanamycin for selection of transformation events, and 10 to 25 mg · L-1 were identified as effective. The cotyledonary nodes and cotyledons from 7-day-old seedlings were used in Agrobacterium-mediated transformations with two kinds of selection strategies, shifting or consistent. Using the shifting selection method (10 mg · L-1 kanamycin, 25 mg · L-1, then back to 10 mg · L-1) cotyledonary nodes gave 10% transformation frequency, and cotyledons 4%, while with the consistent method (25 mg · L-1) lower frequencies were found, 1% for cotyledonary nodes and 0% for cotyledons). Later, in vitro plant axillary buds were tried as explants for transformation, however, transformation frequency was low ranging from 0.5 to 2%. Overall, testing six different vectors and two kinds of Agrobacterium strains, the average transformation frequency using the shifting method was 4.4%. Determining T-DNA insertion numbers by Southern blotting showed that approximately 50% of the transgenic lines had a single-copy insertion. Conclusions: Present research revealed the potential of using crambe meristematic tissue for genetic transformation andin vitro propagation. The most efficient method of transformation used cotyledonary node explants from 7-days-old seedlings with a shifting kanamycin selection. Meristematic tissues (cotyledonary node or axillary bud) had the highest ability for shoot proliferation. Single-copy T-DNA insert lines could be efficiently and reproducibly generated.
    Tomato yellow leaf curl virus resistance by ty-1 involves increased cytosine methylation of viral genomes and is compromised by cucumber mosaic virus infection
    Butterbach, P.B.E. ; Verlaan, M.G. ; Dullemans, A.M. ; Lohuis, H. ; Visser, R.G.F. ; Bai, Y. ; Kormelink, R.J.M. - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)35. - ISSN 0027-8424 - p. 12942 - 12947.
    short interfering rna - dna methylation - geminivirus al2 - l2 proteins - adenosine kinase - gene - suppression - arabidopsis - plants - locus
    Tomato yellow leaf curl virus (TYLCV) and related begomoviruses are a major threat to tomato production worldwide and, to protect against these viruses, resistance genes from different wild tomato species are introgressed. Recently, the Ty-1 resistance gene was identified, shown to code for an RNA-dependent RNA polymerase and to be allelic with Ty-3. Here we show that upon TYLCV challenging of resistant lines carrying Ty-1 or Ty-3, low virus titers were detected concomitant with the production of relatively high levels of siRNAs whereas, in contrast, susceptible tomato Moneymaker (MM) revealed higher virus titers but lower amounts of siRNAs. Comparative analysis of the spatial genomic siRNA distribution showed a consistent and subtle enrichment for siRNAs derived from the V1 and C3 genes in Ty-1 and Ty-3. In plants containing Ty-2 resistance the virus was hardly detectable, but the siRNA profile resembled the one observed in TYLCV-challenged susceptible tomato (MM). Furthermore, a relative hypermethylation of the TYLCV V1 promoter region was observed in genomic DNA collected from Ty-1 compared with that from (MM). The resistance conferred by Ty-1 was also effective against the bipartite tomato severe rugose begomovirus, where a similar genome hypermethylation of the V1 promoter region was discerned. However, a mixed infection of TYLCV with cucumber mosaic virus compromised the resistance. The results indicate that Ty-1 confers resistance to geminiviruses by increasing cytosine methylation of viral genomes, suggestive of enhanced transcriptional gene silencing. The mechanism of resistance and its durability toward geminiviruses under natural field conditions is discussed.
    The evolution of the placenta drives a shift in sexual selection in livebearing fish
    Pollux, B.J.A. ; Meredith, R.W. ; Springer, M.S. ; Garland, T. ; Reznick, D.N. - \ 2014
    Nature 513 (2014). - ISSN 0028-0836 - p. 233 - 236.
    parent-offspring conflict - molecular phylogenetic-relationships - mosquitofish gambusia-holbrooki - reproductive mode - size dimorphism - poeciliidae cyprinodontiformes - maximum-likelihood - viviparity - hypothesis - gene
    The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent–offspring conflicts during pregnancy1, 2, 3, 4. Theory predicts that the rise of these conflicts should drive a shift from a reliance on pre-copulatory female mate choice to polyandry in conjunction with post-zygotic mechanisms of sexual selection2. This hypothesis has not yet been empirically tested. Here we apply comparative methods to test a key prediction of this hypothesis, which is that the evolution of placentation is associated with reduced pre-copulatory female mate choice. We exploit a unique quality of the livebearing fish family Poeciliidae: placentas have repeatedly evolved or been lost, creating diversity among closely related lineages in the presence or absence of placentation5, 6. We show that post-zygotic maternal provisioning by means of a placenta is associated with the absence of bright coloration, courtship behaviour and exaggerated ornamental display traits in males. Furthermore, we found that males of placental species have smaller bodies and longer genitalia, which facilitate sneak or coercive mating and, hence, circumvents female choice. Moreover, we demonstrate that post-zygotic maternal provisioning correlates with superfetation, a female reproductive adaptation that may result in polyandry through the formation of temporally overlapping, mixed-paternity litters. Our results suggest that the emergence of prenatal conflict during the evolution of the placenta correlates with a suite of phenotypic and behavioural male traits that is associated with a reduced reliance on pre-copulatory female mate choice.
    Distribution of anticoagulant rodenticide resistance in Rattus norvegicus in the Netherlands according to Vkorc1 mutations
    Meerburg, B.G. ; Gent-Pelzer, M.P.E. van; Schoelitsz, B. ; Lee, T.A.J. van der - \ 2014
    Pest Management Science 70 (2014)11. - ISSN 1526-498X - p. 1761 - 1766.
    norway rats - tyrosine139cysteine focus - germany - westphalia - chlorophacinone - warfarin - berk. - tests - gene
    BACKGROUND Rodenticide resistance to anticoagulants in Rattus norvegicus will lead to increased difficulties in combating these pest animals. Here, the authors present the results of a survey in the Netherlands where tissue samples and droppings were tested using a newly developed TaqMan PCR test for genotypic variation at codon 139 in the Vkorc1 gene associated with anticoagulant rodenticide resistance. Test results are linked to results of a questionnaire that was conducted among pest controllers. RESULTS Genetic mutations at codon 139 of the Vkorc1 gene in R. norvegicus can be encountered in many parts of the Netherlands. In 34/61 rat tails, a genotype was found that is linked to anticoagulant rodenticide resistance (56%). In droppings, 42/169 samples (25%) showed a resistance-mediating genotype. In addition, indications of a clear genetic substructure in the Netherlands were found. In some regions, only resistance-mediating genotypes were found, corroborating results from the questionnaire in which pest controllers indicated they suspected resistance to anticoagulant rodenticides. CONCLUSION This is the first study to demonstrate the presence of multiple genetic mutations at codon 139 of the Vkorc1 gene in R. norvegicus in the Netherlands. As rodenticides should keep their efficacy because they are a last resort in rodent management, more studies are urgently needed that link specific genetic mutations to the efficacy of active substances. © 2014 Society of Chemical Industry
    Safety assessment of plant varieties using transcriptomics profiling and a one-class classifier
    Dijk, J.P. van; Mello, C.S. de; Voorthuijzen, M.M. ; Hutten, R.C.B. ; Maisonnave Arisi, A.C. ; Jansen, J.J. ; Buydens, L.M.C. ; Voet, H. van der; Kok, E.J. - \ 2014
    Regulatory Toxicology and Pharmacology 70 (2014)1. - ISSN 0273-2300 - p. 297 - 303.
    potato-tubers - microarray data - risk-assessment - food - identification - components - gene
    An important part of the current hazard identification of novel plant varieties is comparative targeted analysis of the novel and reference varieties. Comparative analysis will become much more informative with unbiased analytical approaches, e.g. omics profiling. Data analysis estimating the similarity of new varieties to a reference baseline class of known safe varieties would subsequently greatly facilitate hazard identification. Further biological and eventually toxicological analysis would then only be necessary for varieties that fall outside this reference class. For this purpose, a one-class classifier tool was explored to assess and classify transcriptome profiles of potato (Solanum tuberosum) varieties in a model study. Profiles of six different varieties, two locations of growth, two year of harvest and including biological and technical replication were used to build the model. Two scenarios were applied representing evaluation of a ’different’ variety and a ‘similar’ variety. Within the model higher class distances resulted for the ‘different’ test set compared with the ‘similar’ test set. The present study may contribute to a more global hazard identification of novel plant varieties
    Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
    Daetwyler, H.D. ; Capitan, A. ; Pausch, H. ; Stothard, P. ; Binsbergen, R. van; Brondum, R.F. ; Liao, X. ; Djari, A. ; Rodriguez, S.C. ; Grohs, C. ; Esquerré, D. ; Bouchez, O. ; Rossignol, M.N. ; Klopp, C. ; Rocha, D. ; Fritz, S. ; Eggen, A. ; Bowman, P.J. ; Coote, D. ; Chamberlain, A.J. ; Anderson, C.L. ; Tassel, C.P. ; Hulsegge, B. ; Goddard, M.E. ; Guldbrandsten, B. ; Lund, M.S. ; Veerkamp, R.F. ; Boichard, D.A. ; Fries, R. ; Hayes, B.J. - \ 2014
    Nature Genetics 46 (2014). - ISSN 1061-4036 - p. 858 - 865.
    boophilus-microplus resistance - mitotic chromosomes - genotype imputation - holstein calves - dairy-cattle - milk-yield - bos-taurus - condensin - mutations - gene
    The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle.
    Abscisic acid (ABA) sensitivity regulates desiccation tolerance in germinated Arabidopsis seeds
    Maia de Oliveira, J. ; Dekkers, S.J.W. ; Dolle, M. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
    New Phytologist 203 (2014)1. - ISSN 0028-646X - p. 81 - 93.
    bzip transcription factors - medicago-truncatula seeds - 2c protein phosphatases - signal-transduction - drought tolerance - thaliana - stress - gene - maturation - expression
    During germination, orthodox seeds lose their desiccation tolerance (DT) and become sensitive to extreme drying. Yet, DT can be rescued, in a well-defined developmental window, by the application of a mild osmotic stress before dehydration. A role for abscisic acid (ABA) has been implicated in this stress response and in DT re-establishment. However, the path from the sensing of an osmotic cue and its signaling to DT re-establishment is still largely unknown. Analyses of DT, ABA sensitivity, ABA content and gene expression were performed in desiccation- sensitive (DS) and desiccation-tolerant Arabidopsis thaliana seeds. Furthermore, loss and re-establishment of DT in germinated Arabidopsis seeds was studied in ABA-deficient and ABA-insensitive mutants. We demonstrate that the developmental window in which DT can be re-established correlates strongly with the window in which ABA sensitivity is still present. Using ABA biosynthesis and signaling mutants, we show that this hormone plays a key role in DT re-establishment. Surprisingly, re-establishment of DT depends on the modulation of ABA sensitivity rather than enhanced ABA content. In addition, the evaluation of several ABA-insensitive mutants, which can still produce normal desiccation-tolerant seeds, but are impaired in the re-establishment of DT, shows that the acquisition of DT during seed development is genetically different from its re-establishment during germination.
    Thermoneutrality results in prominent diet-induced body weight differences in C57BL/6J mice, not paralleled by diet-induced metabolic differences
    Hoevenaars, F.P.M. ; Bekkenkamp-Grovenstein, M. ; Janssen, R.J.R.J. ; Heil, S.G. ; Bunschoten, A. ; Hoek-van den Hil, E.F. ; Snaas-Alders, S.H. ; Teerds, K.J. ; Schothorst, E.M. van; Keijer, J. - \ 2014
    Molecular Nutrition & Food Research 58 (2014)4. - ISSN 1613-4125 - p. 799 - 807.
    adipose-tissue - mitochondrial-function - obesity - fat - thermogenesis - models - health - gene - induction - disease
    Scope Mice are usually housed at 20–24°C. At thermoneutrality (28°C) larger diet-induced differences in obesity are seen. We tested whether this leads to large differences in metabolic health parameters. Methods and results We performed a 14-wk dietary intervention in C57BL/6J mice at 28°C and assessed adiposity and metabolic health parameters for a semipurified low fat (10 energy%) diet and a moderate high fat (30 energy%) diet. A large and significant diet-induced differential increase in body weight, adipose tissue mass, adipocyte size, serum leptin level, and, to some extent, cholesterol level was observed. No adipose tissue inflammation was seen. No differential effect of the diets on serum glucose, free fatty acids, triacylglycerides, insulin, adiponectin, resistin, PAI-1, MMP-9, sVCAM-1, sICAM-1, sE-selectin, IL-6, ApoE, fibrinogen levels, or HOMA index was observed. Also in muscle no differential effect on mitochondrial density, mitochondrial respiratory control ratio, or mRNA expression of metabolic genes was found. Finally, in liver no differential effect on weight, triacylglycerides level, aconitase/citrate synthase activity ratio was seen. Conclusion Low fat diet and moderate high fat diet induce prominent body weight differences at thermoneutrality, which is not paralleled by metabolic differences. Our data rather suggest that thermoneutrality alters metabolic homeostasis.
    Rearing history affects behaviour and performance of two virulent Nasonovia ribisnigri populations on two lettuce cultivars
    Broeke, C.J.M. ten; Dicke, M. ; Loon, J.J.A. van - \ 2014
    Entomologia Experimentalis et Applicata 151 (2014)2. - ISSN 0013-8703 - p. 97 - 105.
    nematode meloidogyne-incognita - myzus-persicae hemiptera - host-plant resistance - feeding-behavior - tissue localization - aphid resistance - clones - gene - homoptera - biotypes
    Many aphid species have become virulent to host-plant resistance, which limits the sustainability of insect resistance breeding. However, when this adaptation to resistant plants is associated with fitness costs for the aphids, virulence can be lost in the absence of resistant plants. For two populations of the lettuce aphid, Nasonovia ribisnigri (Mosely) (Hemiptera: Aphididae), we evaluated whether virulence to Nr-gene-based resistance was lost on a susceptible lettuce, Lactuca sativa L. (Asteraceae), and assessed possible costs of virulence. The feeding behaviour and performance of these aphids, reared and tested on susceptible and resistant lettuce, were investigated. The rearing plant affected feeding behaviour and performance of the aphids. Temporary reduction and long-term loss of virulence were found. The total duration of phloem intake was shorter after being reared on susceptible lettuce and tested on resistant lettuce. In addition, one population had a lower survival on resistant lettuce after being reared on susceptible lettuce. There were also indications of fitness costs of the virulence in both populations.
    Mature osteoblasts dedifferentiate in response to traumatic bone injury in the zebrafish fin and skull
    Geurtzen, K. ; Knopf, F. ; Wehner, D. ; Huitema, L.F.A. ; Schulte-Merker, S. ; Weidinger, G. - \ 2014
    Development 141 (2014). - ISSN 0950-1991 - p. 2225 - 2234.
    fibroblast-growth-factor - fracture repair - adult zebrafish - lining cells - regeneration - expression - defects - fate - gene - rats
    Zebrafish have an unlimited capacity to regenerate bone after fin amputation. In this process, mature osteoblasts dedifferentiate to osteogenic precursor cells and thus represent an important source of newly forming bone. By contrast, differentiated osteoblasts do not appear to contribute to repair of bone injuries in mammals; rather, osteoblasts form anew from mesenchymal stem cells. This raises the question whether osteoblast dedifferentiation is specific to appendage regeneration, a special feature of the lepidotrichia bone of the fish fin, or a process found more generally in fish bone. Here, we show that dedifferentiation of mature osteoblasts is not restricted to fin regeneration after amputation, but also occurs during repair of zebrafish fin fractures and skull injuries. In both models, mature osteoblasts surrounding the injury downregulate the expression of differentiation markers, upregulate markers of the pre-osteoblast state and become proliferative. Making use of photoconvertible Kaede protein as well as Cre-driven genetic fate mapping, we show that osteoblasts migrate to the site of injury to replace damaged tissue. Our findings suggest a fundamental role for osteoblast dedifferentiation in reparative bone formation in fish and indicate that adult fish osteoblasts display elevated cellular plasticity compared with mammalian bone-forming cells.
    Exploring causal networks of bovine milk fatty acids in a multivariate mixed model context
    Bouwman, A.C. ; Valente, B.D. ; Janss, L.L.G. ; Bovenhuis, H. ; Rosa, G.J. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X
    somatic-cell score - yield - traits - cattle - gene - associations - parameters - cows
    BACKGROUND: Knowledge regarding causal relationships among traits is important to understand complex biological systems. Structural equation models (SEM) can be used to quantify the causal relations between traits, which allow prediction of outcomes to interventions applied to such a network. Such models are fitted conditionally on a causal structure among traits, represented by a directed acyclic graph and an Inductive Causation (IC) algorithm can be used to search for causal structures. The aim of this study was to explore the space of causal structures involving bovine milk fatty acids and to select a network supported by data as the structure of a SEM. RESULTS: The IC algorithm adapted to mixed models settings was applied to study 14 correlated bovine milk fatty acids, resulting in an undirected network. The undirected pathway from C4:0 to C12:0 resembled the de novo synthesis pathway of short and medium chain saturated fatty acids. By using prior knowledge, directions were assigned to that part of the network and the resulting structure was used to fit a SEM that led to structural coefficients ranging from 0.85 to 1.05. The deviance information criterion indicated that the SEM was more plausible than the multi-trait model. CONCLUSIONS: The IC algorithm output pointed towards causal relations between the studied traits. This changed the focus from marginal associations between traits to direct relationships, thus towards relationships that may result in changes when external interventions are applied. The causal structure can give more insight into underlying mechanisms and the SEM can predict conditional changes due to such interventions.
    Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development
    Cankar, K. ; Kortstee, A.J. ; Toonen, M.A.J. ; Wolters-Arts, M. ; Houbein, R. ; Mariani, C. ; Ulvskov, P. ; Jorgensen, B. ; Schols, H.A. ; Visser, R.G.F. ; Trindade, L.M. - \ 2014
    Plant Biotechnology Journal 12 (2014)4. - ISSN 1467-7644 - p. 492 - 502.
    in-vivo expression - mechanical-properties - potato pectin - arabidopsis - gene - galactan - growth - biosynthesis - mutants - tubers
    Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure–function relationships of pectin in the cell wall, a set of transgenic potato lines with altered pectin composition was analysed. The expression of genes encoding enzymes involved in pectin acetylation, degradation of the rhamnogalacturonan backbone and type and length of neutral side chains, arabinan and galactan in particular, has been altered. Upon crossing of different transgenic lines, some transgenes were not transmitted to the next generation when these lines were used as a pollen donor, suggesting male sterility. Viability of mature pollen was severely decreased in potato lines with reduced pectic arabinan, but not in lines with altered galactan side chains. Anthers and pollen of different developmental stages were microscopically examined to study the phenotype in more detail. Scanning electron microscopy of flowers showed collapsed pollen grains in mature anthers and in earlier stages cytoplasmic protrusions at the site of the of kin pore, eventually leading to bursting of the pollen grain and leaking of the cytoplasm. This phenomenon is only observed after the microspores are released and the tapetum starts to degenerate. Timing of the phenotype indicates a role for pectic arabinan side chains during remodelling of the cell wall when the pollen grain is maturing and dehydrating.
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