457 research outputs found
Measurement of FRFs and Modal Identification In Case of Correlated Multi-Point Excitation
Get PDFThe modal identification of large and dynamically complex structures often requires a multi-point excitation. Sine sweep excitation runs are applied when it is necessary to concentrate more energy on each line of the frequency spectrum. The conventional estimation of FRFs from multi-point excitation requires uncorrelated excitation signals. In case of multi-point (correlated) sine sweep excitation, several sweep runs with altered excitation force patterns have to be performed to estimate the FRFs. An alternative way, which offers several advantages, is to process each sine sweep run separately. The paper first describes the conventional method for FRF estimation in case of multi-point excitation, followed by two alternative methods applicable in case of correlated excitation signals. Both methods generate a virtual single-point excitation from a single run with multi-point excitation. In the first method, an arbitrary structural point is defined as a virtual driving point. This approach requires a correction of the modal masses obtained from modal analysis. The second method utilizes the equality of complex power to generate virtual FRFs along with a single virtual driving point. The computation of FRFs and the modal identification using virtual single-point excitation are explained. It is shown that the correct set of modal parameters can be identified. The application of the methods is elucidated by an illustrative analytical example. It could be shown that the separate evaluation of symmetric and anti-symmetric multi-point excitation runs yield obviously better and more reliable results compared to the conventional method. In addition, the modal analysis of the separate symmetric and anti-symmetric excitation runs is easier, since the stabilization diagrams are easier to interpret. The described methods were successfully applied during the Ground Vibration Tests on Airbus A380 and delivered excellent results. The methods are highly advantageous and may thus be established as a new standard procedure for testing aerospace structures
The fish egg microbiome : diversity and activity against the oomycete pathogen Saprolegnia
No full textY. Liu Prof. dr. F. Govers (promotor); Prof. dr. J.M. Raaijmakers (promotor); Dr. I. de Bruijn (co-promotor); Wageningen University, 13 June 2016, 170 pp. The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia Emerging oomycete pathogens increasingly threaten biodiversity and food security. This thesis describes the study of the microbiome of Atlantic salmon (Salmo salar L.) eggs and analyses of the effects of infections by the oomycete pathogen Saprolegnia on the microbial architecture. A low incidence of Saprolegniosis was correlated with a relatively high abundance and richness of specific commensal Actinobacteria. Among the bacterial community, the isolates Frondihabitans sp. 762G35 (Microbacteriaceae) and Pseudomonas sp. H6 significantly inhibited hyphal attachment of Saprolegnia diclina to live salmon eggs. Chemical profiling showed that these two isolates produce furancarboxylic acid-derived metabolites and a lipopeptide viscosin-like biosurfactant, respectively, which inhibited hyphal growth of S. diclina in vitro. Among the fungal community, the fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride. Both a quantitative and qualitative difference in the Trichoderma population between Saprolegnia-infected and healthy salmon eggs was observed, which suggested that mycoparasitic Trichoderma species could play a role in Saprolegnia suppression in aquaculture. This research provides a scientific framework for studying the diversity and dynamics of microbial communities to mitigate emerging diseases. The Frondihabitans, Pseudomonas and Trichoderma isolates, and/or their bioactive metabolites, are proposed as effective candidates to control Saprolegniosis.</p
Wapenkennis vernieuwt ziektebestrijding (interview met G. Kema en F. Govers)
No full textWageningse onderzoekers kijken naar het DNA van plantenpathogenen om ze in het hart te kunnen treffen, en zo het gebruik van bestrijdingsmiddelen te verminderen. Bij de belangrijkste ziektes in tarwe, banaan en aardappel zoeken ze in het DNA naar cruciale genen voor overleving of voortplanting. Mogelijk kun je een ziekteverwekker ook zijn wapens afneme
Wapenkennis vernieuwt ziektebestrijding (interview met G. Kema en F. Govers)
No full textWageningse onderzoekers kijken naar het DNA van plantenpathogenen om ze in het hart te kunnen treffen, en zo het gebruik van bestrijdingsmiddelen te verminderen. Bij de belangrijkste ziektes in tarwe, banaan en aardappel zoeken ze in het DNA naar cruciale genen voor overleving of voortplanting. Mogelijk kun je een ziekteverwekker ook zijn wapens afneme
The Phytophthora infestans avirulence gene PiaAvr4 and its potato counterpart R4
No full textThe potato late blight disease that is caused by the oomycete pathogen Phytophthora infestans is a major threat for potato crops worldwide. In recent years research on oomycete plant pathogens was boosted by the availability of novel genomic tools and resources for several oomycete genera, such as Phytophthora, Hyaloperonospora, Pythium and Aphanomyces. This has led to the identification of genes involved in diverse biological processes such as sporulation, mating, signaling and pathogenesis. One of the approaches that breeders use to obtain late blight resistant potato cultivars is the introgression of resistance traits from wild Solanum species into the cultivated potato Solanum tuberosum. The pathogen, however, is able to circumvent this resistance; it is often lost shortly after introduction of new cultivars. To better understand the mechanisms underlying this loss of resistance it is of utmost importance to gain insight into the characteristics of the cognate avirulence (Avr) genes of the pathogen. According to the gene-for-gene model Avr genes encode effectors that trigger resistance responses mediated by resistance (R) genes. This thesis first describes the identification of a P. infestans Avr gene, in particular the elicitor activity of the encoded effector protein, the domain structure of the effector and its putative sub-cellular localization. In the second part the recognition specificity of the corresponding R gene and the identification of a marker linked to this R gene are described. Chapter 1 summarizes the advances in oomycete genomics in recent years and the tremendous progress that has been made in gene discovery in oomycete plant pathogens. It describes the different oomycete species that have been studied in more detail and assesses which species are suitable model species for research on oomycete-plant interactions. The identification of the P. infestans avirulence gene PiAvr4 is presented in Chapter 2. PiAvr4, which encodes an RXLR-dEER effector protein, was isolated by positional cloning. AFLP markers were used for landing on BACs and cDNA-AFLP markers pinpointed the gene of interest. Transformation of race 4 strains with PiAvr4 resulted in transformants that are avirulent on the R4 differential of the Mastenbroek differential set (clone Ma-R4). Moreover, in planta expression of PiAvr4 resulted in a necrotic response on clone Ma-R4 but not on plants lacking R4 such as Bintje. All together this proves that PiAvr4 is the avirulence gene that corresponds to the R gene present in clone Ma-R4. In many identified avirulence proteins one or a few amino acid changes in the protein abolish avirulence function. In case of PiAvr4, race 4 strains have frame shift mutations in the open reading frame, resulting in a truncated protein that is not functional as avirulence factor. Effectors within the RXLR-dEER family are rapidly evolving. The selective pressure is targeted predominantly on the C-terminal region of these proteins. Despite this selective pressure the majority of these proteins carry motifs that can be distinguished using Hidden Markov Models searches. They are named W, Y and L motifs after the conserved tryptophan (W), tyrosine (Y) and leucine (L) residues, respectively. As described in Chapter 3 PiAvr4 carries three W motifs and a single Y motif. The motifs together with their flanking regions were tested for activity on Ma-R4 plants. Agroinfection of constructs carrying the W2 motif in combination with either the W1 or W3 motif resulted in a necrotic response. Moreover, we showed that the PiAvr4 homolog PmirAvh4, isolated from Phytophthora mirabilis was also able to elicit a necrotic response on the Ma-R4 potato clone. For several Phytophthora RXLR-dEER effectors it was demonstrated that these proteins are targeted into the host cell and that the RXLR-dEER motif is required for translocation. In Chapter 4 we investigated whether PiAvr4 and IPI-O, like other RXLR-dEER effectors, are also targeted into the host cell. A race 4 P. infestans isolate was transformed with constructs encoding either PiAvr4 or IPI-O fused to a monomeric red fluorescent protein (mRFP) at the C-terminus. Fluorescence microscopy of these transformants showed no specific mRFP fluorescence in free living, non-sporulating mycelium. However, in germinating cysts, the tips of germ tubes and appressoria showed mRFP fluorescence, and during infection of etiolated potato plantlets localized fluorescence was visible at the haustorial neck. Haustoria are highly specialized infection and feeding structures that are in close contact with the plant cell and have a putative role in delivering effector proteins into the host cell. In order to monitor the development of the infection a novel experimental set-up was developed. In this method etiolated in vitro grown potato plantlets are inoculated with P. infestans, which has the advantage that there is no autofluorescence of chlorophyll that masks the mRFP fluorescence and thus disturbs the microscopic analysis in green plant tissues. The lack of chlorophyll does not seem to interfere with infection; zoospores are capable to encyst and to germinate, and the etiolated tissues are readily colonized by P. infestans. The recognition specificity of R4 potato differentials is described in Chapter 5. Initially two different potato clones were developed as R4 differentials; The Mastenbroek differential set, developed in the Netherlands, contains the clone Cebeco44-31-5 (designated as Ma-R4) and the Black differential set, developed in Scotland, contains clone 1563 c (14) (designated as Bl-R4). Virulence assays using several wild type P. infestans strains revealed that the Bl-R4 clone is susceptible to all isolates that are avirulent on clone Ma-R4. Only one single isolate was found to be avirulent on clone Bl-R4, but virulent on Ma-R4. Moreover, in transient expression assays with binary PVX constructs carrying PiAvr4, the Ma-R4 clone but not the Bl-R4 clone responded with an HR. Similar to the R3 locus two different recognition specificities seem to exist for R4. The R3a and R3b genes are located on one locus but whether this is the case for the two R4 genes (named R4Ma and R4Bl, respectively) remains to be determined. Resistance to P. infestans strains carrying PiAvr4 segregates in an 1:1 ratio in two independent potato F1 populations suggesting that R4Ma resistance is determined by a single dominant locus. More in depth studies on the recognition of PiAvr4 by its cognate R protein are hampered by the fact that the resistance gene R4Ma has not yet been identified. In Chapter 6 nucleotide binding site (NBS) profiling was used to generate R4Ma-associated markers. NBS profiling is a biased approach based on PCR amplification of conserved NBS motifs in R genes and R gene homologs. In a bulked segregant analysis, DNA of resistant and susceptible F1 progeny was pooled and used as template for NBS profiling. Several candidate markers were found but eventually one amplified fragment was found to co-segregate with resistance mediated by R4Ma. DNA sequencing of this fragment revealed high similarity to BAC sequences that are mapped to potato chromosome 12. Moreover, the R4Ma marker is homologous to members of the Rx/Gpa2 gene family. Chapter 7 focuses on the secreted effectors of plant pathogenic oomycetes, with special attention to RXLR-dEER effectors, and the role of these proteins in pathogenesis. The RXLR-dEER effector family is rapidly evolving and comprises all secreted oomycete avirulence proteins that are identified up till now. There is now ample evidence that oomycetes utilize the RXLR-dEER domain to deposit effectors inside host cells. Furthermore, this chapter discusses the experimental results described in this thesis in the light of present knowledge on gene-for-gene interactions, effector recognition and late blight resistance. <br/
The interplay between a Phytophthora RXLR effector and an Arabidopsis lectin receptor kinase
No full textPhytophthora infestans – the causal agent of potato late blight – secretes a plethora of effector proteins to facilitate plant infection. The central subject of this thesis is ipiO, one of the first cloned Phytophthora genes with a putative function in pathogenicity as was anticipated based on its in planta induced (ipi) expression, in particular during early stages of host infection. IPI-O contains two striking motifs: RXLR-dEER and RGD. RGD is a cell adhesion motif and was shown to be involved in binding to the extracellular lectin domain of LecRK-I.9, a lectin receptor kinase of Arabidopsis. The RXLR-dEER motif plays a role in effector trafficking into host cells and is shared by several secreted oomycete effector proteins which are known to function as race-specific avirulence (Avr) factors. In a previous study, that was aimed at identifying novel pairs of P. infestans Avr and host plant resistance (R) genes, a high-throughput effector genomics screen identified ipiO as Avr-blb1, the counterpart of the late blight R gene Rpi-blb1 which originates from the nightshade Solanum bulbocastanum. Often R genes exploited in late blight resistance breeding become rapidly ineffective as a result of adaptation of P. infestans. However, unlike most late blight R genes that interact in a gene-for-gene manner with Avr genes, Rpi-blb1 seemed to have the potential to remain its effectiveness. In section 2 we monitored the genetic variation and distribution of the ipiO family in an extensive isolate collection of P. infestans and closely related species. This resulted in the identification of 16 IPI-O variants that could be sub-divided in three distinct classes. Variants from class I and class II were shown to induce cell death when co-infiltrated with Rpi-blb1 in Nicotiana benthamiana. Class III consists solely of the highly divergent variant IPI-O4, that is not able to trigger Rpi-blb1-mediated cell death. Class I is highly diverse and represented in all P. infestans isolates analyzed so far, except in two Mexican P. infestans isolates. The latter two are capable to infect Rpi-blb1 plants, suggesting that the lack of class I variants in the genome of these strains allows them to escape recognition by Rpi-blb1 plants. We propose that profiling of the ipiO variants within P. infestans populations can predict the effectiveness of Rpi-blb1-mediated resistance in potato and, as such, can facilitate integrated disease management. Section 3 of this thesis deals with legume-like lectin receptor kinases (LecRKs), membrane-spanning proteins with potential roles in adaptive responses and cell wall integrity. We present an inventory and a phylogenetic analysis of the Arabidopsis LecRK gene family. The rationale behind this study was to gain better insight into the diversity of LecRKs and their potential roles in plant defense. A comprehensive expression analysis based on exploration of existing databases revealed that several LecRK genes are induced upon treatment with elicitors or during pathogen infection. Based on the phylogenetic analysis we have reclassified the LecRK genes and proposed a new nomenclature. LecRK-I.9, one of the clade I Arabidopsis LecRKs which binds the RGD cell adhesion motif of IPI-O, was shown to mediate adhesion between the cell wall (CW) and plasma membrane (PM). In contrast, IPI-O disrupts these adhesions by virtue of its RGD motif. We analyzed Arabidopsis LecRK-I.9 knock-out lines (lecrk-I.9) for their response to pathogen infection, in particular to Phytophthora brassicae. We also analyzed transgenic Arabidopsis lines expressing ipiO, and observed that both the ipiO-expressing lines and lecrk-I.9 lines are impaired in their resistance to oomycete pathogens. To unravel the mechanisms underlying this phenomenon we analysed callose deposition upon MAMP (i.e. flg22) treatment and investigated the strength of CW-PM adhesions under plasmolysis-inducing conditions. The results indicated that LecRK-I.9 is not only important for the maintenance of the CW-PM continuum, but also in MAMP-triggered immunity. Also here, both the ipiO-expressing lines and the lecrk-I.9 knock-outs displayed a destabilized CW-PM continuum and impaired callose deposition, and hence, they can be regarded as phenocopies. Arabidopsis plants that constitutively express LecRK-I.9 were smaller in size, and displayed increased levels of anthocyanin and lignin. Additionally, these lines were shown to exhibit enhanced resistance to P. brassicae. Furthermore, we studied transgenic potatoes that constitutively Arabidopsis LecRK-I.9. In comparison to the parental control potato line the transgenic lines were less susceptible to mild and moderately aggressive P. infestans isolates, but the increased tolerance was not sufficient to provide resistance to aggressive isolates. These results strongly suggest that LecRK-I.9 is a novel resistance component that plays a role in defense against Phytophthora. In Section 4 we describe a novel method for propagating P. brassicae zoospores on an intermediate host plant. This resulted in the production of high numbers of zoospores thereby facilitating highly reproducible small and large scale inoculation experiments. This thesis is completed with a general discussion (Section 5) addressing the current understanding of effector uptake by host cells, the subsequent recognition by cognate R proteins mediating effector-triggered immunity, and RXLR-dEER effector diversity. We also discuss the role of the RGD motif in effectors of both animal and plant pathogens, and the potential functions of LecRKs. Finally, we high-light the advantages of Arabidopsis-Phytophthora pathosystems as research object. <br/
Conservation implications of <i>Sabellaria spinulosa</i> reef patches in a dynamic sandy-bottom environment
Get PDFBiogenic reefs form biodiversity hotspots and are key components of marine ecosystems, making them priority habitats for nature conservation. However, the conservation status of biogenic reefs generally depends on their size and stability. Dynamic, patchy reefs may therefore be excluded from protection. Here, we studied epibenthos and epifauna density, richness, and community composition of patchy, dynamic Sabellaria spinulosa (ross worm) reefs in the North Sea. This study was conducted by comparing boxcore (endobenthos) and video transect (epifauna) data from two research campaigns in 2017 and 2019 to the Brown Bank area on the Dutch Continental Shelf, where S. spinulosa reefs were first discovered in 2017. The Brown Bank area is characterized by dynamic, migratory bedforms at multiple scales which potentially affect biogenic reef stability. We showed that S. spinulosa habitats had a patchy distribution and alternated with habitats comprised of plain sand. Average S. spinulosa habitat patch size was 5.57 ± 0.99 m and 3.94 ± 0.22 m in 2017 and 2019 respectively (mean ± SE), which especially in 2019 closely resembled the small-scale megaripple bedforms. Contrary to the endobenthos communities that were unaffected by S. spinulosa, epifauna density and species richness were at least two times higher in S. spinulosa habitats compared to sandy habitats, resulting in different community compositions between the two habitat types. We showed that S. spinulosa persisted in the area for almost 2 years. Although the stability of individual patches remained unclear, we demonstrated that even patchy biogenic reefs may promote density and local biodiversity of mobile, epibenthic species, very likely as a result of increased habitat heterogeneity provided by reef habitat patches. This indicates that patchy biogenic reefs that occur in dynamic environments may also have high ecological value and their conservation status should be (re)considered to ensure their protection
Measuring centimeter-scale sand ripples using multibeam echosounder backscatter data from the Brown Bank area of the Dutch continental shelf
Get PDFBackscatter data from multibeam echosounders are commonly used to classify seafloor sediment composition. Previously, it was found that the survey azimuth affects backscatter when small organized seafloor structures, such as sand ripples, are present. These sand ripples are too small to be detected in the multibeam bathymetry. Here, we show that such azimuth effects are time dependent and are useful to examine the orientation of sand ripples in relation to the flow direction of the tide. To this end, multibeam echosounder data at four different frequencies were gathered from the area of the Brown Bank in the North Sea. The acoustic results were compared to video and tide-flow data for validation. The sand ripples affected the backscatter at all frequencies, but for the lowest frequencies the effect was spread over more beam angles. Using the acoustic data made it possible to deduce the orientations of the sand ripples over areas of multiple square kilometers. We found that the top centimeter(s) of the seafloor undergoes a complete transformation every six hours, as the orientation of the sand ripples changes with the changing tide. Our methodology allows for morphology change detection at larger scales and higher resolutions than previously achieved
The Existence and Origin of Multiple Equilibria in Sand-Mud Sediment Beds
Get PDFThe sediment composition of the seabed governs its mobility, hence determining sediment transport and morphological evolution of estuaries and tidal basins. Bed sediments often consist of mixtures of sand and mud, with spatial gradients in the sand/mud content. This study aims at increasing the understanding of processes driving the sediment composition in tidal basins, focusing on depositional processes. We show that bed sediments in the Wadden Sea tend to be either mud-dominated or sand-dominated, resulting in a bimodal distribution of the mud content where the two modes represent equilibrium conditions. The equilibria depend primarily on the sediment deposition fluxes, with bimodality originating from the dependence of suspended sand/mud concentrations on the local bed composition. Our analysis shows that bimodality is a phenomenon that is not only specific for the Wadden Sea; it can be expected for a wide range of suspended sediment concentrations and thus also in other systems worldwide.Coastal EngineeringEnvironmental Fluid Mechanic
The genus Phytophthora; phylogeny, speciation and host specificity
No full textPormotie-onderzoek naar de fylogenie, soortsvorming en waardplantspecificiteit in het geslacht Phytophthora
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