Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

Current refinement(s):

Records 1 - 20 / 337

  • help
  • print

    Print search results

  • export
    A maximum of 250 titles can be exported. Please, refine your queryYou can also select and export up to 30 titles via your marked list.
  • alert
    We will mail you new results for this query: keywords==dna
Check title to add to marked list
Disentangling hexaploid genetics : towards DNA-informed breeding for postharvest performance in chrysanthemum
Geest, Geert van - \ 2017
University. Promotor(en): Richard Visser, co-promotor(en): Uulke van Meeteren; Paul Arens. - Wageningen : Wageningen University - ISBN 9789463436427 - 142
chrysanthemum - plant breeding - postharvest quality - hexaploidy - polyploidy - quantitative trait loci - phenotypes - linkage mapping - metabolomics - polymorphism - dna - plantenveredeling - kwaliteit na de oogst - hexaploïdie - polyploïdie - loci voor kwantitatief kenmerk - fenotypen - koppelingskartering - metabolomica - polymorfisme

DNA-informed selection can strongly improve the process of plant breeding. It requires the detection of DNA polymorphisms, calculation of genetic linkage, access to reliable phenotypes and methods to detect genetic loci associated with phenotypic traits of interest. Cultivated chrysanthemum is an outcrossing hexaploid with an unknown mode of inheritance. This complicates the development of resources and methods that enable the detection of trait loci. Postharvest performance is an essential trait in chrysanthemum, but is difficult to measure. This makes it an interesting but challenging trait to phenotype and detect associated genetic loci. In this thesis I describe the development of resources and methods to enable phenotyping for postharvest performance, genetic linkage map construction and detection of quantitative trait loci in hexaploid chrysanthemum.

Postharvest performance is a complicated trait because it is related to many different disorders that reduce quality. One of these disorders in chrysanthemum is disk floret degreening, which occurs after long storage. In chapter 2, we show that degreening can be prevented by feeding the flower heads with sucrose, suggesting carbohydrate starvation plays a role in the degreening process. To investigate the response to carbohydrate starvation of genotypes with different sensitivity to disk floret degreening, we investigated the metabolome of sugar-fed and carbohydrate-starved disk florets by 1H-NMR and HPAEC. We show that the metabolome is severely altered at carbohydrate starvation. In general, starvation results in an upregulation of amino acid and secondary metabolism. Underlying causes of genotypic differences explaining variation in disk floret degreening in the three investigated genotypes remained to be elucidated, but roles of regulation of respiration rate and camphor metabolism were posed as possible candidates.

In chapter 3, disk floret degreening was found to be the most important postharvest disorder after 3 weeks of storage among 44 white chrysanthemum cultivars. To investigate the inheritance of disk floret degreening, we crossed two genotypes with opposite phenotypic values of both disk floret degreening and carbohydrate content to obtain a population segregating for disk floret degreening. To phenotype the cultivar panel and the bi-parental population precisely and in a high throughput manner, we developed a method that quantified colour of detached capitula over time. This method was validated with visual observations of disk floret degreening during vase life tests. In a subset of the bi-parental population we measured carbohydrate content of the disk florets at harvest. The amount of total carbohydrates co-segregated with sensitivity to degreening, which shows that the difference in disk floret degreening sensitivity between the parents could be explained by their difference in carbohydrate content. However, the correlation was rather weak, indicating carbohydrate content is not the only factor playing a role.

In order to develop resources for DNA-informed breeding, one needs to be able to characterize DNA polymorphisms. In chapter 4, we describe the development of a genotyping array containing 183,000 single nucleotide polymorphisms (SNPs). These SNPs were acquired by sequencing the transcriptome of 13 chrysanthemum cultivars. By comparing the genomic dosage based on the SNP assay and the dosage as estimated by the read depth from the transcriptome sequencing data, we show that alleles are expressed conform the genomic dosage, which contradicts to what is often found in disomic polyploids. In line with this finding, we conclusively show that cultivated chrysanthemum exhibits genome-wide hexasomic inheritance, based on the segregation ratios of large numbers of different types of markers in two different populations.

Tools for genetic analysis in diploids are widely available, but these have limited use for polyploids. In chapter 5, we present a modular software package that enables genetic linkage map construction in tetraploids and hexaploids. Because of the modularity, functionality for other ploidy levels can be easily added. The software is written in the programming language R and we named it polymapR. It can generate genetic linkage maps from marker dosage scores in an F1 population, while taking the following steps: data inspection and filtering, linkage analysis, linkage group assignment and marker ordering. It is the first software package that can handle polysomic hexaploid and partial polysomic tetraploid data, and has advantages over other polyploid mapping software because of its scalability and cross-platform applicability.

With the marker dosage scores of the bi-parental F1 population from the genotyping array and the developed methods to perform linkage analysis we constructed an integrated genetic linkage map for the hexaploid bi-parental population described in chapter 3 and 4. We describe this process in chapter 6. With this integrated linkage map, we reconstructed the inheritance of parental haplotypes for each individual, and expressed this as identity-by-descent (IBD) probabilities. The phenotypic data on disk floret degreening sensitivity that was acquired as described in chapter 3, was used in addition to three other traits to detect quantitative trait loci (QTL). These QTL were detected based on the IBD probabilities of 1 centiMorgan intervals of each parental homologue. This enabled us to study genetic architecture by estimating the effects of each separate allele within a QTL on the trait. We showed that for many QTL the trait was affected by more than two alleles.

In chapter 7, the findings in this thesis are discussed in the context of breeding for heterogeneous traits, the implications of the mode of inheritance for breeding and the advantages and disadvantages of polyploidy in crop breeding. In conclusion, this thesis provides in general a significant step for DNA-informed breeding in polysomic hexaploids, and for postharvest performance in chrysanthemum in particular.

Studying fast dynamics in biological complexes : from photosynthesis in vivo to single DNA molecules in vitro
Farooq, Shazia - \ 2017
University. Promotor(en): Herbert van Amerongen, co-promotor(en): Johannes Hohlbein. - Wageningen : Wageningen University - ISBN 9789463431002 - 149
biology - dna - proteins - interactions - probability analysis - förster resonance energy transfer - fluorescence - spectroscopy - photosynthesis - biologie - eiwitten - interacties - waarschijnlijkheidsanalyse - förster resonantie-energieoverdracht - fluorescentie - spectroscopie - fotosynthese

During the last decades, fluorescence spectroscopy has emerged as a powerful tool in the fields of biophysics, biotechnology, biochemistry, cellular biology and the medical sciences. These techniques are highly sensitive, and allow us to study the structure and dynamics of (bio)molecular systems (Valeur 2001). A significant advantage of fluorescence techniques is that they can often be non-invasive and measurements can be performed in real time. In this thesis different advanced fluorescence methods will be used to study two important biological processes: (1) DNA dynamics and (2) plant photosynthesis. The first part aims at improving the smFRET technique for the analysis of DNA dynamics and other fast conformational changes. This improvement is made by combining and developing instrumentation and data evaluation tools. The second part is the continuous development of time-resolved fluorescence spectroscopy methods, as well their application in the field of photosynthesis to study ultrafast processes in thylakoid membranes and leaves. The two fluorescence techniques are technically and conceptually very different, but they are both designed for analysis of biomolecular systems. In this thesis, the techniques are applied to study energy transfer and dynamical changes in DNAs, thylakoid membranes and leaves.

REFERENCE: VALEUR B 2001. Molecular Fluorescence: Principles and Applications. 1 ed: Wiley-VCH.

The aging immune system and nutritional interventions
Beek, Adriaan A. - \ 2017
University. Promotor(en): Huub Savelkoul; R.W. Hendriks, co-promotor(en): P.J.M. Leenen; Harry Wichers. - Wageningen : Wageningen University - ISBN 9789462579552 - 250
immune system - senescence - gastrointestinal microbiota - basophils - macrophages - dna - nutritional intervention - immuunsysteem - veroudering - microbiota van het spijsverteringskanaal - basofielen - macrofagen - maatregel op voedingsgebied

The increased numbers of elderly people pose a major burden to public health care and society. DNA damage is considered to be the major origin of age-related changes in the body. With aging, the immune system becomes deregulated and is characterized by a low-grade inflammation (inflammaging). In this thesis, we investigate the effects of nutritional and microbial interventions on the aging immune system.

In chapter 2, we elaborate on the role of basophils in the immune system, particularly in the initiation and perpetuation of allergic immune responses. We found that basophils and dendritic cells interact in vitro, which reciprocally affects their surface markers and cytokine production. Thus, by modulating cytokine production and surface marker expression on dendritic cells, basophils may act as accessory cells in immune responses. Because little is known about the effects of aging on basophils, we investigated in chapter 3 whether basophils are affected with aging. We found that frequencies of basophils in the spleen of aging mice are increasing, while their phenotype in bone marrow and spleen changes. Moreover, to investigate the role of microbiota in the aging process, we studied the effects of microbiota transfer from young or aged mice into germfree mice. Aging, and microbiota from aged mice, in particular affect differentiation and function of basophil precursors. These findings warrant further studies on the role of basophils in T helper-2 immune responses with aging.

The contribution of macrophages to inflammaging is described in chapter 4. Important aspects for macrophage polarization and function, like autophagy and cellular metabolism, are discussed. Targeting of aged macrophages by (nutritional) interventions may open up new therapeutic opportunities for elderly.

In chapter 5, we studied the in vitro interaction between bacterial supplementations and immune cells (whole spleen cells and macrophages). We noticed that aged immune cells mount a different response to bacterial strains than young immune cells. Based on these outcomes, we selected three bacterial strains (Lactobacillus plantarum WCFS1, Lactobacillus casei BL23, Bifidobacterium breve DSM20213) for in vivo application in chapter 6. We used Ercc1-/Δ7 mice, which lack fully functional ERCC1 protein. As a consequence, DNA repair is compromised, which results in accelerated aging features in all organs, including the immune system. We supplemented Ercc1-/Δ7 mice, as well as control Ercc1+/+ mice with the three selected bacterial strains. We observed that L. plantarum prevented the age-related decline in mucus barrier function of Ercc1-/Δ7 mice, whereas B. breve exacerbated the age-related decline in mucus barrier. L. casei supplementation elevated multiple systemic inflammatory markers in Ercc1-/Δ7 mice, including Ly6Chi monocytes, neutrophils, and Th17 cells in spleen. Strikingly, we found major changes in the mucus barrier and immune system after supplementation of Ercc1-/Δ7 mice with L. plantarum and L. casei, but not after supplementation of Ercc1+/+ mice. Therefore, we conclude that caution is needed in the selection of candidate probiotic strains for supplementation of aging individuals.

In chapter 7, we took a different approach to modulate the aging immune system by applying dietary tryptophan restriction in Ercc1+/+ and Ercc1-/Δ7 mice. We observed that in both mouse models dietary tryptophan restriction modulated B cell development and microbiota composition. In particular, we found a near-complete absence of B cell precursors in the bone marrow after dietary tryptophan restriction. The decline in B cell precursors was correlated with decreased abundance of the Akkermansia and Alistipes bacterial strains in the intestine. Thus, our results show that dietary tryptophan restriction is a powerful intervention to shape immunity and gut microbiota, also in aging. In chapter 8, we assessed the role of microbiota in the aging gut and immune system. Microbiota from young and aged mice were transferred to germfree mice. Aged microbiota induced higher T helper-1 cell and regulatory T cell frequencies in the spleen. In the ileum, the expression of inflammatory markers was increased after transferring aged microbiota, accompanied by differences in the abundance of microbial species. We conclude that senescent microbiota contribute to the inflammaging observed in aging mice.

In chapter 9, we discuss the findings presented in this thesis, concluding with directions for future research. In summary, our studies show that the aging gut and immune system of mice can be modulated by nutritional and/or microbial interventions. Interestingly, our mouse models clearly provide evidence that age-related effects could be reverted or prevented by these interventions. Nevertheless, our studies at the same time show the need for translational research in order to apply the presented dietary and microbial interventions in elderly.

Structural basis for specific gene regulation by Auxin Response Factors
Freire Rios, Alejandra - \ 2016
University. Promotor(en): Dolf Weijers. - Wageningen : Wageningen University - ISBN 9789462579538 - 190
auxins - gene regulation - plant growth regulators - embryonic development - plant embryos - dna - auxinen - genregulatie - plantengroeiregulatoren - embryonale ontwikkeling - plantenembryo's

Auxin is a plant hormone that triggers a broad variety of responses during plant development. These responses range from correct cell division patterns during embryogenesis to formation and growth of different organs. Due to its importance for plant growth and development, many aspects of the biology of auxin have been studied. In Chapter 2, we use Arabidopsis embryogenesis as a stage to describe generalities about its biosynthesis, transport, components of its signaling pathway and transcriptional control of some know target genes.

As most of the players involved in transcriptional regulation in response to auxin have been identified, the question of how the same signal can elicit so many different responses remains open. In this thesis we approach this issue by focusing on the ultimate effectors of the auxin signaling pathway: the ARF family of transcription factors. In Chapter 3 we present the crystal structure of the DNA binding Domain (DBD) of two divergent members of the family: ARF1 and ARF5. Careful observation of the structures, followed by in vitro and in vivo experiments led to the following conclusions: 1) ARF DBDs dimerize through a conserved alpha-helix, and bind cooperatively to an inverted repeat of the canonical TGTCTC AuxRE. Dimerization of this domain is important for high-affinity DNA binding and in vivo activity. 2) Monomeric ARFs have the same binding preference for the DNA sequence TGTCGG (determined by protein binding microarray). 3) DNA-contacting residues are almost completely conserved within the ARF family members. 4) The distance between the AuxREs may play a role for binding of specific ARF dimers as for example, ARF5 can accommodate and bind to different spacing (6-9 bp) compared to ARF1 which is more rigid (7-8 bp).

In Chapter 4 we follow up on the observations made. First we again used structural biology to determine the reason of the high binding affinity to the TGTCGG sequence compared to the previously identified canonical TGTCTC element. We found that in complex with TGTCGG, His137 (ARF1) could rotate and make hydrogen bonds with either G5 or G6, as well as a hydrogen bond with the C opposing to G6. This rotation is not possible when in complex with TGTCTC and there the same histidine can make only one hydrogen bond with the G opposing to C6. We conclude then that this histidine plays a role in determining the strength of binding to TGTCNN elements and that this also reflects in its specific transcriptional activity as mutating the corresponding histidine in ARF5 renders a semi-functional protein in vivo (Chapter 3).

The next observation we followed up in Chapter 4 is the biological meaning of ARF DBDcooperative binding to DNA. We identified AuxRE inverted repeats (IR) in the promoter of the TMO5 gene and mutated them. This brought the expression of the gene to very low levels despite the presence of other multiple single AuxREs. Thus, the single inverted AuxRE repeat in the TMO5 promoter is essential for ARF5 binding and gene regulation. Importantly, mutating only a single AuxRE element within the inverted repeat led to very pronounced loss of activity, consistent with requirement of both AuxRE sites for high-affinity ARF5 binding. We then concluded that IR AuxREs have a significant effect in gene regulation by ARFs. Next we search the genome for bipartite AuxREs that correlated to auxin response and found two main elements: inverted repeat with 8 bases of spacing (IR8) and direct repeat with 5 bases of spacing (DR5). As this kind of bipartite AuxREs are rarer to find than single AuxREs, we tested their presence in promoters as predictors of auxin responsiveness by qPCR. We found that about 75% of the selected genes containing either IR8 or DR5 responded to auxin. The expression study also show that genes containing the DR5 sequence were only up-regulated when regulated. Interestingly, Surface Plasmon Resonance study showed that only class A (activator) ARFs can bind the DR5 sequence cooperatively.

As the structural differences of ARFs DBDs are subtle, we then asked if specific gene targeting is determined by this domain alone. In Chapter 5 we used a DBD swap experiment and conclude that the DBD is necessary for specific gene targeting but not sufficient and the other domains of an ARF also contribute in its specific activity.

In Chapter 5 we expand our focus from the DBD to the other ARF domains, Middle Region (MR) and C-terminal (CT). As ARFs have protein-protein interaction interfaces in all three domains, we expressed the isolated domains of ARF5 and perform immuno-precipitation followed by tandem mass-spectrometry. Although the procedure needs optimization, some interactions expected for each domain could be identified. The DBD showed to interact with the general transcription machinery and the CT could interact with another ARF and 3 Aux/IAA. These interactions seem to be specific as the Aux/IAA recovered are not the most abundant in the sampled tissue.

Finally, in Chapter 6 all the obtained results are put in a broader context and new questions derived from our results are proposed.

Co-assembled DNA-protein polymer bottlebrushes : main-chain stiffening & liquid crystallinity
Storm, I.M. - \ 2016
University. Promotor(en): Martien Cohen Stuart; Frans Leermakers, co-promotor(en): Renko de Vries. - Wageningen : Wageningen University - ISBN 9789462577466 - 161 p.
polymers - liquid crystals - dna - proteins - polymeren - vloeibare kristallen - eiwitten

Bottlebrushes are macromolecules consisting of a backbone polymer onto which side chains are either physically or chemically grafted. Early theories suggested that attaching side chains to a (flexible) backbone molecule would induce the so-called main-chain stiffening effect. This newly formed bottlebrush molecule should therefore behave as a semi-flexible polymer rather than a flexible polymer. Due to this semi-flexible behaviour bottlebrushes should also be able to show liquid crystalline behaviour. However, there are very few examples of bottlebrush systems that are able to make liquid crystalline phases. In this thesis, we present a co-assembled bottlebrush system that consist of DNA as the backbone molecule and genetically engineered protein polymers as side chains. This co-assembled system is one of the few bottlebrush systems that actually does show liquid crystalline behaviour. This ability makes this bottlebrush system a perfect system to explain why it is so very difficult to make liquid crystalline phases with bottlebrushes. We have shown that attaching side chains will, at first, result in an effectively more flexible bottlebrush system. Only for systems with very densely packed and long side chains is the stiffness of the bottlebrush molecule increasing. Moreover, with osmotic stress experiments we have shown that the presence of free polymers also has a negative influence on the stiffness of bottlebrush molecules and hence this reduces the tendency for the system to form liquid crystals.

Genetic diversity and evolution in Lactuca L. (Asteraceae) : from phylogeny to molecular breeding
Wei, Z. - \ 2016
University. Promotor(en): Eric Schranz. - Wageningen : Wageningen University - ISBN 9789462576148 - 210 p.
lactuca sativa - leafy vegetables - phylogeny - genetic diversity - domestication - molecular breeding - genomes - dna - quantitative trait loci - evolution - bladgroenten - fylogenie - genetische diversiteit - domesticatie - moleculaire veredeling - genomen - loci voor kwantitatief kenmerk - evolutie

Cultivated lettuce (Lactuca sativa L.) is an important leafy vegetable worldwide. However, the phylogenetic relationships between domesticated lettuce and its wild relatives are still not clear. In this thesis, I focus on the phylogenetic relationships within Lactuca L., including an analysis of the wild Lactuca species that are endemic to Africa for the first time. The genetic variation of responses to salinity in a recombinant inbred line population, derived from a cross between the lettuce crop (L. sativa ‘Salinas’) and wild species (L. serriola), was investigated and the candidate gene in the identified QTL regions was further studied.

In Chapter 1, I introduce and discuss topics related to genetic diversity and evolution in Lactuca, including an overview of lettuce cultivars and uses, its hypothesized domestication history, the taxonomic position of Lactuca, current status of molecular breeding in lettuce and mechanisms of salinity tolerance in plants, especially the High-affinity K+ Transporter (HKT) gene family.

In Chapter 2, the most extensive molecular phylogenetic analysis of Lactuca was constructed based on two chloroplast genes (ndhF and trnL-F), including endemic African species for the first time. This taxon sampling covers nearly 40% of the total Lactuca species endemic to Africa and 34% of all Lactuca species. DNA sequences from all the subfamilies of Asteraceae in Genbank and those generated from Lactuca herbarium samples were used to elucidate the monophyly of Lactuca and the affiliation of Lactuca within Asteracaeae. Based on the subfamily tree, 33 ndhF sequences from 30 species and 79 trnL-F sequences from 48 species were selected to infer phylogenetic relationships within Lactuca using Randomized Axelerated Maximum Likelihood (RAxML) and Bayesian Inference (BI) analyses. In addition, biogeographical, chromosomal and morphological character states were analysed based on the Bayesian tree topology. The results showed that Lactuca contains two distinct phylogenetic clades - the crop clade and the Pterocypsela clade. Other North American, Asian and widespread species either form smaller clades or mix with the Melanoseris species in an unresolved polytomy. The newly sampled African endemic species probably should be excluded from Lactuca and treated as a new genus.

In Chapter 3, twenty-seven wild Lactuca species and four outgroup species were sequenced using next generation sequencing (NGS) technology. The sampling covers 36% of total Lactuca species and all the important geographical groups in the genus. Thirty chloroplast genomes, including one complete (partial) large single copy region (LSC), one small single copy region (SSC), one inverted repeat (IR) region, and twenty-nine nuclear ribosomal DNA sequences (containing the internal transcribed spacer region ) were successfully assembled and analysed. A methodology paper for which I am co-author, but is not included in this thesis, of the sequencing pipeline was published: ‘Herbarium genomics: plastome sequence assembly from a range of herbarium specimens using an Iterative Organelle Genome Assembly (IOGA) pipeline’. These NGS data helped resolve deeper nodes in the phylogeny within Lactuca and resolved the polytomy from Chapter 2. The results showed that there are at least four main groups within Lactuca: the crop group, the Pterocypsela group, the North American group and the group containing widely-distributed species. I also confirmed that the endemic African species should be removed and treated as a new genus.

In Chapter 4, quantitative trait loci (QTLs) related to salt-induced changes in Root System Architecture (RSA) and ion accumulation were determined using a recombinant inbred line population derived from a cross between cultivated lettuce and wild lettuce. I measured the components of RSA by replicated lettuce seedlings grown on vertical agar plates with different NaCl concentrations in a controlled growth chamber environment. I also quantified the concentration of sodium and potassium in replicates of greenhouse-grown plants watered with 100 mM NaCl. The results identified a total of fourteen QTLs using multi-trait linkage analysis, including three major QTLs associated with general root development (qRC9.1), root growth in salt stress condition (qRS2.1), and ion accumulation (qLS7.2).

In Chapter 5, one of the identified QTL regions (qLS7.2) reported in Chapter 4 was found to contain a homolog of the HKT1 from Arabidopsis thaliana. I did a phylogenetic analysis of Lactuca HKT1-like protein sequences with other published HKT protein sequences and determined transmembrane and pore segments of lettuce HKT1;1 alleles, according to the model proposed for AtHKT1;1. Gene expression pattern and level of LsaHKT1;1 (L. sativa ‘Salinas’) and LseHKT1;1 (L. serriola) in root and shoot were investigated in plants growing hydroponically over a time-course. The measurements of Na+ and K+ contents were sampled at the same time as the samples used for gene expression test. In addition, I examined the 5’ promoter regions of the two genotypes. The results showed low expression levels of both HKT1;1 alleles in Lactuca root and relatively higher expression in shoot, probably due to the negative cis-regulatory elements of HKT1 alleles found in Lactuca promoter regions. Significant allelic differences were found in HKT1;1 expression in early stage (0-24 hours) shoots in and in late stage (2-6 days) roots. shoot HKT1;1 expression/root HKT1;1 expression was generally consistent with the ratios of Na+/K+ balance in the relevant tissues (shoot Na+/K+ divided by root Na+/K+).

In Chapter 6, I summarize and discuss the results from previous chapters briefly. The implications of Chapter 2 and 3 for Lactuca phylogenetics are discussed, including some key characters for the diagnosis of species within Lactuca, the use of herbarium DNA for NGS technology, and perspectives into Lactuca phylogeny. Future perspectives of genome-wide association mapping for lettuce breeding were also discussed. Lastly, I propose to integrate phylogenetic approaches into investigations of allelic differences in lettuce, not just associated with salinity stress but also with other stressed and beneficial characters, both within and between species.

DNA : the recipe book for all the processes in the plant : all cells have the same generic information
Heuvelink, E. ; Kierkels, T. - \ 2015
In Greenhouses : the international magazine for greenhouse growers 4 (2015)4. - ISSN 2215-0633 - p. 12 - 13.
dna - plantenveredeling - genetische modificatie - transfer rna - messenger rna - ribosomen - eiwitten - aminozuren - enzymen - mutaties - plant breeding - genetic engineering - ribosomes - proteins - amino acids - enzymes - mutations
It’s sometimes called a blueprint: DNA, the carrier of genetic information. But the term recipe book covers it better. It explains how the plant can respond to changing conditions. Plant breeders take advantage of natural variations in DNA. Genetic modification can make their job easier.
Wat is erfelijkheid?
Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, Kor - \ 2015
Zeldzaam huisdier 40 (2015)3. - ISSN 0929-905X - p. 10 - 12.
heritability - rassen (dieren) - dierveredeling - dna - eigenschappen - spermatozoön - eicellen - bevruchting - genen - allelen - homozygoten - heterozygoten - mutaties - genetische merkers - breeds - animal breeding - properties - spermatozoa - ova - fertilization - genes - alleles - homozygotes - heterozygotes - mutations - genetic markers
Eigenschappen van dieren zijn in meer of mindere mate erfelijk. Ze gaan over van ouders op nakomelingen. Maar ervaren fokkers weten dat in de fokkerij 1+1 geen 2 is. Welke wetmatigheden en welke toevalligheden spelen een rol in de erfelijkheid? Wat heeft het DNA-onderzoek ons daar recentelijk over geleerd en wat kunnen we daarmee?
Elucidating the Ramularia eucalypti species complex
Videira, S.I.R. ; Groenewald, J.Z. ; Kolecka, A. ; Haren, L. van; Boekhout, T. ; Crous, P.W. - \ 2015
Persoonia 34 (2015). - ISSN 0031-5850 - p. 50 - 64.
desorption ionization-time - flight mass-spectrometry - primer sets - identification - phylogeny - pathogens - fungi - dna - epidemiology - punctiformis
The genus Ramularia includes numerous phytopathogenic species, several of which are economically important. Ramularia eucalypti is currently the only species of this genus known to infect Eucalyptus by causing severe leaf-spotting symptoms on this host. However, several isolates identified as R. eucalypti based on morphology and on nrDNA sequence data of the ITS region have recently been isolated from other plant hosts, from environmental samples and also from human clinical specimens. Identification of closely related species based on morphology is often difficult and the ITS region has previously been shown to be unreliable for species level identification in several genera. In this study we aimed to resolve this species-complex by applying a polyphasic approach involving morphology, multi-gene phylogeny and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). Six partial genes (ITS, ACT, TEF1-a, HIS3, GAPDH and RPB2) were amplified and sequenced for a total of 44 isolates representing R. eucalypti and closely related species. A multi-gene Bayesian phylogenetic analysis and parsimony analysis were performed, and both the resulting trees showed significant support for separation of seven species in R. eucalypti, including two previously described (R. eucalypti and R. miae), four novel species here described (R. haroldporteri, R. glennii, R. mali and R. plurivora) and one undescribed Ramularia species (sterile). Additionally, Mycosphaerella nyssicola is newly combined in Ramularia as R. nyssicola. Main mass spectra (MSPs) of several R. eucalypti strains were generated using MALDI-TOF MS and were compared through a Principal Component Analysis (PCA) dendogram. The PCA dendrogram supported three clades containing R. plurivora, R. glenni/R. mali and R. eucalypti/R. miae. Although the dendrogram separation of species differed from the phylogenetic analysis, the clinically relevant strains were successfully identified by MALDI-TOF MS
Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856
Thompson, O.A. ; Snoek, L.B. ; Nijveen, H. ; Sterken, M.G. ; Volkers, R.J.M. ; Brenchley, R. ; Hof, A. van 't; Bevers, R.P.J. ; Cossins, A.R. ; Yanai, I. ; Hajnal, A. ; Schmid, T. ; Perkins, J.D. ; Spencer, D. ; Kruglyak, L. ; Andersen, E.C. ; Moerman, D.G. ; Hillier, L.W. ; Kammenga, J.E. ; Waterston, R.H. - \ 2015
Genetics 200 (2015)3. - ISSN 0016-6731 - p. 975 - 989.
natural variation data - c. elegans - arabidopsis-thaliana - gene - polymorphism - populations - diversity - nematodes - dna - evolutionary
The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
Physiologically based in silico modelling to examine DNA adduct formation by different food-borne a,ß-unsaturated aldehydes at realistic low dietary exposure levels
Kiwamoto, R. - \ 2015
University. Promotor(en): Ivonne Rietjens, co-promotor(en): Ans Punt. - Wageningen : Wageningen University - ISBN 9789462572843 - 200
aldehyden - dna - ontgifting - voedseladditieven - aromatische stoffen - genotoxiciteit - carcinogenen - modellen - wiskundige modellen - fysiologie - simulatiemodellen - toxicologie - aldehydes - detoxification - food additives - flavourings - genotoxicity - carcinogens - models - mathematical models - physiology - simulation models - toxicology

Abstract (R.Kiwamoto ISBN 978-94-6257-284-3)

Various α,β-unsaturated aldehydes are present in fruits, vegetables, spices, or processed products containing these items as natural constituents or as added food flavouring agents. Because of the α,β-unsaturated aldehyde moiety the β carbon in the molecule becomes electron deficient and the aldehydes react with electron rich molecules including DNA via Michael addition. The formation of DNA adducts raises a concern for genotoxicity, although formation of DNA adducts may not be significant at low doses relevant for dietary exposure in vivo because of adequate detoxification. This thesis therefore aimed at determining dose-dependent detoxification and DNA adduct formation of food-borne α,β-unsaturated aldehydes by using a physiologically based in silico modelling approach in order to contribute to the safety assessment of these aldehydes used as food flavourings instead of performing animal experiments.

Physiologically based in silico models were developed for 18 α,β-unsaturated aldehydes. The model outcomes indicated that the DNA adduct formation by the 18 α,β-unsaturated aldehydes as food flavourings is negligible and does not raise a safety concern at their levels of intake resulting from their use as food flavourings. The application of QSAR models strongly accelerated the development process of the PBK/D models of the group of 18 compounds. Also, it was illustrated that physiologically based in silico models provide a very useful and powerful tool to facilitate a group evaluation and read-across for food-borne DNA reactive agents. PBK/D models developed for the group of compounds supported read-across from cinnamaldehyde which is known not to be genotoxic or carcinogenic in vivo to other aldehydes, by allowing comparison of dose-dependent DNA adduct formations. Altogether this thesis presented physiologically based in silico modelling as an approach to test relevance of positive in vitro genotoxicity results by DNA reactive compounds in vivo without using animal experiments.

Exposing the grey seal as a major predator of harbour porpoises
Leopold, M.F. ; Begeman, L. ; Bleijswijk, J. van; IJsseldijk, L. ; Witte, H.J. ; Grone, A. - \ 2015
Proceedings of the Royal Society. B: Biological Sciences 282 (2015)1798. - ISSN 0962-8452 - 7 p.
halichoerus-grypus - phocoena-phocoena - natural mortality - escape tactics - southern gulf - st-lawrence - risk - dna
Harbour porpoises (Phocoena phocoena) stranding in large numbers around the southern North Sea with fatal, sharp-edged mutilations have spurred controversy among scientists, the fishing industry and conservationists, whose views about the likely cause differ. The recent detection of grey seal (Halichoerus grypus) DNA in bite marks on three mutilated harbour porpoises, as well as direct observations of grey seal attacks on porpoises, have identified this seal species as a probable cause. Bite mark characteristics were assessed in a retrospective analysis of photographs of dead harbour porpoises that stranded between 2003 and 2013 (n = 1081) on the Dutch coastline. There were 271 animals that were sufficiently fresh to allow macroscopic assessment of grey seal-associated wounds with certainty. In 25% of these, bite and claw marks were identified that were consistent with the marks found on animals that had tested positive for grey seal DNA. Affected animals were mostly healthy juveniles that had a thick blubber layer and had recently fed. We conclude that the majority of the mutilated harbour porpoises were victims of grey seal attacks and that predation by this species is one of the main causes of death in harbour porpoises in The Netherlands. We provide a decision tree that will help in the identification of future cases of grey seal predation on porpoises.
Genomics and the challenging translation into conservation practice
Shafer, A.B.A. ; Wolf, J.B.W. ; Alves, P.C. ; Bergstrom, L. ; Bruford, M.W. ; Brannstrom, I. ; Colling, G. ; Dalen, L. van; Meester, L. de; Ekblom, R. ; Vergeer, P. - \ 2015
Trends in Ecology and Evolution 30 (2015)2. - ISSN 0169-5347 - p. 78 - 87.
genetic diversity - background selection - population genomics - insular population - dna - divergence - speciation - evolution - sequence - markers
The global loss of biodiversity continues at an alarming rate. Genomic approaches have been suggested as a promising tool for conservation practice as scaling up to genome-wide data can improve traditional conservation genetic inferences and provide qualitatively novel insights. However, the generation of genomic data and subsequent analyses and interpretations remain challenging and largely confined to academic research in ecology and evolution. This generates a gap between basic research and applicable solutions for conservation managers faced with multifaceted problems. Before the real-world conservation potential of genomic research can be realized, we suggest that current infrastructures need to be modified, methods must mature, analytical pipelines need to be developed, and successful case studies must be disseminated to practitioners.
Genomic sequencing and microsatellite marker development for Boswellia papyrifera, an economically important but threatened tree native to dry tropical forests
Addisalem, A.B. ; Esselink, G. ; Bongers, F. ; Smulders, M.J.M. - \ 2015
AoB Plants 7 (2015). - ISSN 2041-2851 - 11 p.
populus-nigra l. - conservation genetics - frankincense - populations - ethiopia - database - plants - reads - tool - dna
Microsatellite (or simple sequence repeat, SSR) markers are highly informative DNA markers often used in conservation genetic research. Next-generation sequencing enables efficient development of large numbers of SSR markers at lower costs. Boswellia papyrifera is an economically important tree species used for frankincense production, an aromatic resinous gum exudate from bark. It grows in dry tropical forests in Africa and is threatened by a lack of rejuvenation. To help guide conservation efforts for this endangered species, we conducted an analysis of its genomic DNA sequences using Illumina paired-end sequencing. The genome size was estimated at 705 Mb per haploid genome. The reads contained one microsatellite repeat per 5.7 kb. Based on a subset of these repeats, we developed 46 polymorphic SSR markers that amplified 2-12 alleles in 10 genotypes. This set included 30 trinucleotide repeat markers, four tetranucleotide repeat markers, six pentanucleotide markers and six hexanucleotide repeat markers. Several markers were cross-transferable to Boswellia pirrotae and B. popoviana. In addition, retrotransposons were identified, the reads were assembled and several contigs were identified with similarity to genes of the terpene and terpenoid backbone synthesis pathways, which form the major constituents of the bark resin.
Genetische monitoring van de Nederlandse otterpopulatie 2013/2014 : ontwikkeling van populatieomvang en populatiegenetische status
Kuiters, A.T. ; Groot, G.A. de; Lammertsma, D.R. ; Jansman, H.A.H. ; Bovenschen, J. - \ 2015
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2624) - 39
lutra lutra - otters - fauna - populatiedichtheid - populatiegenetica - inteelt - mortaliteit - dna - monitoring - friesland - noordwest-overijssel - drenthe - population density - population genetics - inbreeding - mortality
Jaarlijks wordt in opdracht van het ministerie van Economische Zaken de Nederlandse otterpopulatie genetisch gemonitord. Daarmee wordt een vinger aan de pols gehouden wat betreft de ontwikkeling van de genetische status van de populatie. Deze vorm van monitoring, gebaseerd op DNA-profielen op basis van DNA geïsoleerd uit verse spraints (uitwerpselen), maakt het tevens mogelijk veranderingen in de ruimtelijke verspreiding en de populatieomvang van jaar tot jaar te volgen. De monitoringsronde van 2013/2014 laat zien dat de populatie verder is gegroeid naar een aantal van ca. 140 individuen. Echter, de genetische variatie binnen individuen is sterker afgenomen vergeleken met voorafgaande jaren. Onderdeel van deze monitoring is ook autopsie van dode otters, waarbij wordt gekeken naar de doodsoorzaak en de belangrijkste lichaamskenmerken. Knelpuntlocaties waar otters worden doodgereden worden in beeld gebracht. Er is een sterke toename van het jaarlijkse aantal verkeersslachtoffers. Deze lijkt gelijke tred te houden met de toename van de populatieomvang.
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.
Phylogenetic relationships within Fritillaria section Petilium based on AFLP fingerprints
Wietsma, W.A. ; Deinum, D. ; Teunissen, H. ; Berg, R.G. van den - \ 2015
Plant Systematics and Evolution 301 (2015)3. - ISSN 0378-2697 - p. 1043 - 1054.
liliaceae - dna
Fritillaria sect. Petilium (Fritillaria L., Liliaceae), consists of four species: F. chitralensis, F. eduardii, F. imperialis and F. raddeana. We studied their phylogenetic relationships with AFLP’s, crossing experiments and morphological observations. The AFLP data confirm that F. eduardii is a separate species and not a variety of F. imperialis. Within F. eduardii the two earlier distinguished varieties can indeed be recognised. Our AFLP results also show that F. chitralensis, originally described as F. imperialis var. chitralensis, is different from F. imperialis and is a species in its own right. The results of the AFLP’s and the crossing experiments show that within F. imperialis two varieties can be recognised, one variety containing representatives that possesses the so called ‘foxy’ smell, and a second variety with odourless representatives. A new name for this odourless variety is proposed
Detection of Single-Nucleotide Polymorphisms in Plasmodium falciparum by PCR Primer Extension and Lateral Flow Immunoassay
Moers, A.P.H.A. ; Hallett, R.L. ; Borrow, R. ; Schallig, H.D.F.H. ; Sutherland, C.J. ; Amerongen, A. van - \ 2015
Antimicrobial Agents and Chemotherapy 59 (2015)1. - ISSN 0066-4804 - p. 365 - 371.
real-time pcr - carbon nanoparticles - malaria - dna - chloroquine - assay - amplification - sensitivity - resistance - travelers
The resistance of Plasmodium falciparum to some antimalarial drugs is linked to single-nucleotide polymorphisms (SNPs). Currently, there are no methods for the identification of resistant parasites that are sufficiently simple, cheap, and fast enough to be performed at point-of-care, i.e., in local hospitals where drugs are prescribed. Primer extension methods (PEXT) were developed to identify 4 SNPs in P. falciparum positioned at amino acids 86, 184, and 1246 of the P. falciparum multidrug resistance 1 gene (pfmdr1) and amino acid 76 of the chloroquine resistance transporter gene (pfcrt). The PEXT products were visualized by a nucleic acid lateral flow immunoassay (NALFIA) with carbon nanoparticles as the detection labels. PCR-PEXT-NALFIAs showed good correlation to the reference methods, quantitative PCR (qPCR) or direct amplicon sequence analysis, in an initial open-label evaluation with 17 field samples. The tests were further evaluated in a blind study design in a set of 150 patient isolates. High specificities of 98 to 100% were found for all 4 PCR-PEXT genotyping assays. The sensitivities ranged from 75% to 100% when all PEXT-positive tests were considered. A number of samples with a low parasite density were successfully characterized by the reference methods but failed to generate a result in the PCR-PEXT-NALFIA, particularly those samples with microscopy-negative subpatent infections. This proof-of principle study validates the use of PCR-PEXT-NALFIA for the detection of resistance-associated mutations in P. falciparum, particularly for microscopy-positive infections. Although it requires a standard thermal cycler, the procedure is cheap and rapid and thus a potentially valuable tool for point-of-care detection in developing countries
Characterization of apoptosis in PER.C6® batch and perfusion cultures
Mercier, S.M. ; Diepenbroek, B. ; Martens, D.E. ; Wijffels, R.H. ; Streefland, M. - \ 2015
Biotechnology and Bioengineering 112 (2015)3. - ISSN 0006-3592 - p. 569 - 578.
hamster ovary cells - high-level expression - flow-cytometry - line per.c6 - death - adenovirus - dna - vaccine - gene - manufacture
Preventing or delaying cell death is a challenge in mammalian cell cultures for the development and optimization of production processes for biopharmaceuticals. Cell cultures need to be maintained highly viable for extended times in order to reach maximum production yields. Moreover, programmed cell death through apoptosis is often believed to occur without being detected by classical viability measurements. In this study, we characterized cell death in PER.C6® batch and perfusion cultures using three flow cytometry techniques measuring different steps of the apoptosis cascade: DNA fragmentation, caspases activation and phosphatidylserine externalization. We showed that apoptosis is the main pathway of PER.C6® cell death in batch cultures after depletion of main carbon sources. In high cell density perfusion cultures fed at a constant specific perfusion rate, both high viability and very limited apoptosis were observed. When extending this perfusion process far beyond standard operations, cultures were exposed to suboptimal process conditions, which resulted in an increase of apoptotic cell death. Moreover, we showed that the reference viability measurement using trypan blue exclusion properly assesses the level of cell death in PER.C6® cultures. This study is a first step in understanding the mechanisms of PER.C6® cell death, which will be helpful to support applications of the cell line.
Richard Immink": 'Van tulp en lelie weten we nog steeds heel weinig'
Dwarswaard, A. - \ 2014
BloembollenVisie (2014)299. - ISSN 1571-5558 - p. 22 - 22.
bloembollen - tulpen - lelies - landbouwkundig onderzoek - plantengenetica - dna - ornamental bulbs - tulips - lilies - agricultural research - plant genetics
Bijna twee jaar geleden werd prof. dr. ir. Richard Immink voor een dag in de week benoemd tot “bollenprof”. Samen met twee assistenten-in-opleiding voert hij fundamenteel onderzoek uit aan tulp en lelie. Tijd voor een tussenbalans in drie afleveringen. In deze eerste aflevering legt Richard Immink uit waar het in dit project om draait: genetische geheimen ontrafelen van tulp en lelie.
Check title to add to marked list
<< previous | next >>

Show 20 50 100 records per page

Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.