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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    Rekenregels rundvee voor de Landbouwtelling : verantwoording van het gebruik van het Identificatie & Registratiesysteem
    Os, J. van; Bartholomeus, M.G.T.M. ; Jeurissen, L.J.J. ; Reenen, C.G. van - \ 2017
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 91) - 68
    rundveehouderij - rundvee - landbouwtellingen - emissie - registratie - identificatie - bedrijfsstructuur in de landbouw - nederland - cattle husbandry - cattle - agricultural censuses - emission - registration - identification - farm structure - netherlands
    Om te voldoen aan statistische verplichtingen voor veehouderij en bedrijfsstructuur en voor de registratievan emissies is informatie nodig over de rundveehouderij in Nederland. Daartoe vraagt de Rijksoverheid bijveehouders op hoeveel rundvee aanwezig is, uitgesplitst in verschillende diergroepen; dit is een onderdeelvan de jaarlijkse landbouwtelling. De Rijksoverheid streeft naar beperking van administratieve lastendruk bijondernemers. Wageningen Environmental Research heeft op verzoek van het ministerie van EconomischeZaken onderzocht in welke mate het mogelijk is om de benodigde gegevens af te leiden uit het bestaandeIdentificatie & Registratiesysteem (I&R) Rundveehouderij (een systeem voor identificatie en registratie vandieren voor dier- en volksgezondheid). Dat blijkt grotendeels goed haalbaar; voor de meeste bedrijvenkunnen alle diergroepen automatisch uit I&R bepaald worden. Voor sommige bedrijven is een aanvullendeverdeling van diergroepen over productiedoelen nodig. Deze nieuwe werkwijze leidt niet alleen tot lagereadministratieve lasten, maar ook tot een kwaliteitsverbetering van de rundveegegevens.---Information on cattle farming in the Netherlands is needed for the national statistics on beef and dairy farmsand farm structure. To obtain this information the national government asks farmers to submit informationon the number of cattle on their farms, divided into the various animal classes, as part of the annualagricultural census. The government also wants to minimise the administrative burden on farmers. At therequest of the Ministry of Economic Affairs, Wageningen Environmental Research has studied to what extentit would possible to derive the required information from the existing identification and registration system(I&R) for beef and dairy farms (a system for identifying and registering livestock for animal and humanhealth purposes). The results show that this is largely possible: for most farms all the animal classes can beautomatically derived from the I&R. For some farms it is necessary to make an additional division of animalclasses by product category. This new way of working will not only reduce the administrative burden, but itwill also lead to better quality data on beef and dairy cattle.
    Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
    Bergh, Erik van den - \ 2017
    Wageningen University. Promotor(en): M.E. Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
    capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - capparaceae - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

    As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

    Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

    In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

    In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

    Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

    In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

    ZooEasy als registratiesysteem voor zeldzame rassen
    Oldenbroek, J.K. ; Eijndhoven, M.H.T. - \ 2015
    Zeldzaam huisdier 40 (2015)1. - ISSN 0929-905X - p. 16 - 17.
    dierveredeling - identificatie - zeldzame rassen - rassen (dieren) - hondenrassen - vogels - stamboom - stamboeken - geitenrassen - fokken van kleine dieren - computer software - internet - animal breeding - identification - rare breeds - breeds - dog breeds - birds - pedigree - herdbooks - goat breeds - small animal rearing - computer software - internet
    Nauwkeurige registratie is een vereiste voor een verantwoorde en
    succesvolle fokkerij. Niet alleen speelt afstamming bij zeldzame rassen
    een cruciale rol, fokkers willen ook gegevens over het exterieur
    en de prestaties van de dieren overzichtelijk vastleggen. In deze
    serie worden de mogelijkheden van een aantal systemen toegelicht.
    Rapportage kwalitatief onderzoek 'Identificatie en Registratie van honden'
    Niekerk, T.G.C.M. van; Potters, P. ; Meeusen, M.J.G. - \ 2014
    Wageningen : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 818) - 27
    honden - gezelschapsdieren - identificatie - registratie - dierenwelzijn - puppy's - diergezondheid - huisdieren - dogs - pets - identification - registration - animal welfare - puppies - animal health - domestic animals
    Het onderhavige rapport is een verslag van een kwalitatief onderzoek onder (potentiële) hondenbezitters met als belangrijkste doelstelling om inzicht krijgen in de kennis, houding en gedrag van (huidige en toekomstige) hondenbezitters t.a.v. het chippen en registeren van honden.
    Ecologie stengelaaltjes
    Vreeburg, P.J.M. ; Dees, R.H.L. ; Doorn, J. van; Boer, F.A. de - \ 2014
    Lisse : Praktijkonderzoek Plant & Omgeving, Business Unit Bloembollen, Boomkwekerij & Fruit - 27
    bloembollen - plantenplagen - nematoda - ditylenchus dipsaci - detectie - methodologie - identificatie - levenscyclus - dierecologie - ornamental bulbs - plant pests - nematoda - ditylenchus dipsaci - detection - methodology - identification - life cycle - animal ecology
    Bij een besmetting met stengelaaltjes (Ditylenchus dipsaci) in bolgewassen is de economische schade groot, omdat het een quarantaine-organisme betreft. Binnen deze aaltjessoort zijn verschillende rassen te onderscheiden, met elk een andere waardplantenreeks. Het tulpenstengelaaltje heeft de breedste waardplantenreeks en is daarmee ook het meest gevreesde ras. Om onderzoek te doen naar de overleving, verspreiding en bestrijding van stengelaaltjes, zijn technieken nodig voor rassenidentificatie, in stand houding en vermeerdering van de aaltjes. Het ontbreken van geschikte technieken vormt een grote belemmering voor het onderzoek. Dit project heeft nieuwe methoden opgeleverd voor de bewaring en detectie van (tulpen-)stengelaaltjes.
    'Producentenorganisatie heeft onderzoekers scherp gemaakt' "Nieuw elan in de varkenssector komt het onderzoek ten goede, vindt Geert van der Peet
    Peet, G.F.V. van der - \ 2014
    Boerderij 100 (2014)5. - ISSN 0006-5617 - p. 45 - 45.
    varkenshouderij - duurzaamheid (sustainability) - innovaties - identificatie - dierenwelzijn - pig farming - sustainability - innovations - identification - animal welfare
    Nieuw elan on de varkenssector komt het onderzoek ten goede, vindt Geert van der Peet, themaleider duurzame veehouderij voor de topsector Agri & Food bij Wageningen UR.
    Food traceability: traceability systems and species identification
    Spiegel, M. van der; Alewijn, M. ; Dijk, J.P. van; Fels-Klerx, H.J. van der; Kok, E.J. ; Molenaar, B. ; Prins, T.W. ; Roest, J.G. van der; Ruth, S.M. van; Scholtens-Toma, I.M.J. ; Voorhuijzen, M.M. ; Zaaijer, S. - \ 2014
    naspeurbaarheid - voedselveiligheid - identificatie - voedseltechnologie - tracking en tracing - traceability - food safety - identification - food technology - tracking and tracing
    Poster on RIKILT and food traceability.
    Phylogeny and DNA-based identification in Phoma and related genera
    Aveskamp, M.M. - \ 2014
    Wageningen University. Promotor(en): Pedro Crous; Pierre de Wit. - Wageningen : Wageningen University - ISBN 9789461739148 - 206
    phoma - fylogenie - taxonomie - moleculaire taxonomie - identificatie - verklarende woordenlijsten - phoma - phylogeny - taxonomy - molecular taxonomy - identification - glossaries

    This thesis treats the taxonomy of a generic complex presently known as PhomaSacc. emend Boerema & Bollen. This group of fungi comprises more than 200 taxa at species or variety level that are characterised by the production of hyaline, non-septate conidial spores in pycnidial conidiomata. The genus is omnipresent in the environment, and exponents can be found on a wide range of host substrates.

    For many years the genus Phomawas the main research topic of a group of mycologists at the Dutch National Plant Protection Service. The studies conducted in the last decennia of the previous century culminated in a handbook that monographed the majority of the species in the above-mentioned generic complex. This handbook marked the end of the era in which the taxonomy of this genus mainly relied on morphological observations and cultural descriptions. However, it can also be regarded as the starting point of the present study. The aim of the present project was to integrate DNA-based identification methods into the taxonomic system established by the previously mentioned group of researchers. The major part of this study therefore deals with the validation of current generic and species concepts.

    An extensive literature review of the biology, taxonomy and identification methods to the species in this genus is provided in Chapter 2, with specific reference to the progress that has been made in Phomataxonomy after the publication of the abovementioned handbook. The advantages and disadvantages of the current taxonomical system are discussed. Furthermore, this chapter describes the general biology of the species in this fungal group, including their life cycles, distribution and host substrates. The importance of the genus for plant health and quarantine issues is illustrated, and the development of a rapid and robust identification technique based on DNA barcodes is advocated.

    Chapter 3treats species in Phomasection Peyronellaea. Species in this section are typified by the production of dictyochlamydospores, and thus have additional morphological characters to use in taxon delineation in comparison with species in the other Phomasections. All species in this group were subjected to a morphological re-examination and phylogenetic analyses employingITS, actin, and β-tubulin nucleotide sequences. Based on multi-gene analyses, Phomasection Peyronellaeacould not be maintained as a taxonomic entity, due to the polyphasic nature of taxa in this section. The morphological study revealed that for five species a taxonomic revision was required. A further five species appeared to be new to science, including Ph. microchlamydospora, Ph. omnivirens, and Ph. schachtii. Also the taxonomic noveltiesPh. coffeae-arabicaeand Ph. sancta are described here, and are allocated to the genus Peyronellaea, re-erected in Chapter 5.

    In Chapter 4the diversity among species and varieties belonging to the Ph. exiguaspecies complex is investigated. The Ph. exiguaspecies complex includes nine taxa at varietal level and four species that have a high morphological similarity both in vivoand in vitro, whilst historical relations with plant hosts cannot be maintained. Among this group, both omnipresent saprobes as well as host-specific plant pathogens are present – including the potato pathogen Ph. foveata.

    The diversity in this complex is studied by means of Internal Transcribed Spacer regions 1 & 2 and intervening 5.8S nrDNA (ITS) and actin nucleotidesequence analyses and a DNA fingerprinting technique rarely used to study fungal diversity. This technique, DNA Amplification Fingerprinting (DAF) employs short, arbitrary primers that form a loop, or a mini-hairpin, under specific temperature conditions and is frequently used in molecular plant breeding. The amplified DNA fragments were isolated and sequenced in order to develop taxon-specific markers and primer combinations based on the SCARs (Sequence Characterised Amplified Regions) and actin sequence data generated. These tools can aid rapid identification of this morphologically highly similar set of taxa.

    Two separate taxa were recognised within the type variety Ph. exiguavar. exigua. In the following chapter these taxa are described and all species and varieties in this complex are recombined into the new genus Boeremia.

    Chapter 5provides further details about the taxonomy and phylogeny of the species of interest, with a special focus on the taxa that are phylogenetically placed with Didymellaceae. In total 206 taxa were treated, of which 159 have affinities with Phoma.

    The genus is circumscribed in the first section of this chapter. The phylogeny was reconstructed using 28S nrDNA (Large Subunit) and 18S nrDNA (Small Subunit) sequence data. It was shown that the currently used Boeremaean subdivision of the phomoid taxa and the phylogeny were inconsistent, as the genus was highly polyphyletic. Species belonging to the form-genus Phomawere retrieved in as much as six distinct clades within Pleosporales. These clades even represent different families. The majority of the phomoid taxa, including the type species Ph. herbarumand most exponents of the sections Macrospora, Peyronellaea, Heterospora, and Phyllostictioides, were found in a single clade that represented the Didymellaceae. Most species that are associated with the Phomasections Plenodomusand Pilosacluster with the Leptosphaeriaceaeand Pleosporaceaeclades. Furthermore, some species were also found to cluster in the Sporormiaceaeand Cucurbitariaceaeclades.

    In the second part of this chapter, the phylogenetic variation of the species and varieties in Didymellaceaeis further assessed, using a phylogenetic reconstruction that is based on DNA sequences of the Large Subunit, ITS, and part of the β-tubulin (TUB) gene region. Besides the teleomorph genus Didymella, members of the teleomorph genera Leptosphaerulinaand Macroventuriawere also found to cluster in this clade. Based on the reconstructed phylogeny, Didymellaceaesegregate into at least 18 distinct clusters, of which many can be associated with specific morphological characters. Furthermore, a number of taxa did not match any of these clusters, suggesting that an evolutionary correct subdivision of the Phomaspecies in Didymellaceaeis even more complex. Taxa in four of these phylogenetic clusters were also defined well enough by means of morphology to elevate these groups to new or reinstalled genera, namely Stagonosporopsis, Epicoccum, Boeremiaand Peyronellaea. A total of 61 taxa were recombined and several new species of Phomawere introduced, namely Ph. brasiliensis, Ph. bulgarica, Ph. dactylidis, Ph. dimorpha, Ph. longicolla, Ph. minor, Ph. pedeiaeand Ph. saxea. Furthermore, two new varieties were described, Boeremia exigua var. gilvescensand B. exigua var. pseudolilacis.

    Finally, the results presented in this dissertation are highlighted and discussed inChapter 6. In total 13 species of Phomaand two taxa at varietal level were newly described during the course of this study. Moreover the taxonomic status of species in the form-genus Phomawere further clarified, and insight provided into the phylogenetic status of Didymellaceae, a fungal family that was recently established, comprising most species of Phoma, Ascochytaand Didymella. All macro- and micromorphological data obtained in this study, as well as the DNA sequences, were placed online in a publicly available polyphasic identification database (www.q-bank.eu). This will enable scientists and institutes involved in plant health to correctly identify phomoid species. Rapid identification of these species based on the tools and data generated in this study, can facilitate swift clearing of plant material and arable products during export and import, and prevent the spread of quarantine organisms.

    Voedselfraudeur ontmaskerd (interview met Saskia van Ruth en Rita Boerrigter-Eenling)
    Smit, A. ; Ruth, S.M. van; Boerrigter-Eenling, G.R. - \ 2014
    WageningenWorld 2014 (2014)1. - ISSN 2210-7908 - p. 28 - 31.
    biologische voedingsmiddelen - authenticiteit - dranken - voedselanalyse - identificatie - voedseltechnologie - melkproducten - voedselinspectie - organic foods - authenticity - beverages - food analysis - identification - food technology - milk products - food inspection
    Producenten die sjoemelen met de herkomst van levensmiddelen kunnen vaker op het matje worden geroepen. RIKILT Wageningen UR ontwikkelt steeds meer tests die duidelijk maken waar de ingrediënten vandaan komen én of ze wel echt op biologische wijze zijn gemaakt. Koffie en eieren blijken wat dat betreft verrassend herkenbaar.
    De Nederlandse Bijen
    Belgers, J.D.M. - \ 2013
    Bijenhouden 2013 (2013)juni. - ISSN 1877-9786 - p. 4 - 5.
    apidae - honingbijen - nederland - bestuivers (dieren) - drachtplanten - dierecologie - determinatietabellen - identificatie - boekbesprekingen - apidae - honey bees - netherlands - pollinators - pollen plants - animal ecology - keys - identification - book reviews
    Het Jaar van de Bij (2012) was een groot succes. Alom aandacht voor zowel de honingbij als de wilde bij. Bijenhotels rezen het afgelopen jaar als paddenstoelen uit de grond; veel mensen weten nu het verschil tussen honingbij, wilde (solitaire) bij en wesp. Hoogtepunt voor veel bijenliefhebbers was de presentatie van het boek ‘De Nederlandse Bijen’op 13 december 2012 bij Naturalis in Leiden. Na onze vooraankondiging in januari hier een bespreking van een kenner.
    Cultivation and diseases of Proteaceae: Leucadendron, Leucospermum and Protea
    Crous, P.W. ; Denman, S. ; Taylor, J.E. ; Swart, L. ; Bezuidenhout, C.M. ; Hoffman, L. ; Palm, M.E. ; Groenewald, J.Z. - \ 2013
    Utrecht, The Netherlands : CBS-KNAW Fungal Biodiversity Centre (CBS biodiversity series 13) - ISBN 9789070351953 - 360
    proteaceae - leucadendron - leucospermum - protea - snijbloemen - teelt - plantenziekten - plantenziekteverwekkende schimmels - taxonomie - identificatie - determinatietabellen - gastheerreeks - plantenziekteverwekkende bacteriën - ziektebestrijding - fytosanitair beleid - verwelkingsziekten - wortelrot - kanker (plantenziektekundig) - proteaceae - leucadendron - leucospermum - protea - cut flowers - cultivation - plant diseases - plant pathogenic fungi - taxonomy - identification - keys - host range - plant pathogenic bacteria - disease control - phytosanitary policies - wilts - root rots - cankers
    Proteaceae represent a prominent family of flowering plants in the Southern Hemisphere. Because of their beauty, unique appearance, and relatively long shelf life, Proteaceae cut-flowers have become a highly desirable crop for the export market. The cultivation of Proteaceae is a thriving industry that provides employment in countries where these flowers are grown, often in areas that are otherwise unproductive agriculturally. Diseases cause a loss in yield, and also limit the export of these flowers due to strict phytosanitary regulations. In this publication the fungi that cause leaf, stem and root diseases on Leucadendron, Leucospermum and Protea are treated. Data are provided pertaining to the taxonomy, identification, host range, distribution, pathogenicity, molecular characteristics and control of these pathogens. Taxonomic descriptions and illustrations are provided and keys are included to distinguish species in genera where a number of species affect Proteaceae. Disease symptoms are described and colour photographs are included. Where known, factors that affect disease epidemiology are discussed. Disease management strategies are also presented that will assist growers and advisors in making appropriate choices for reducing disease in specific areas. Information is also provided relating to crop improvement, cultivation techniques, harvesting and export considerations. Further development and expansion of this industry depends on producing and obtaining disease-free germplasm from countries where these plants are indigenous. For that reason it is important to document the fungi that occur on Proteaceae, and to establish the distribution of these fungi. These data are essential for plant quarantine services for use in risk assessments.
    Milk biomarker discovery for detection of recombinant bovine somatotropin abuse
    Ludwig, S.K.J. ; Smits, N.G.E. ; Nielen, M.W.F. - \ 2013
    somatotropine - melkeiwit - melkkoeien - biomarkers - identificatie - somatotropin - milk protein - dairy cows - biomarkers - identification
    The objective of the research is the identification of proteins in milk, whose concentrations are significantly increased or decreased after treating dairy cows with rbST. These identified milk protein biomarkers will be the basis of a screening method to detect rbST doping in dairy cows.
    Covering ground: insights into soil ecology by molecular monitoring of nematode assemblages
    Vervoort, M.T.W. - \ 2013
    Wageningen University. Promotor(en): Jaap Bakker, co-promotor(en): Hans Helder. - S.l. : s.n. - ISBN 9789461736277 - 118
    vrijlevende nematoden - bodemecologie - identificatie - moleculaire ecologie - bodemmonitoring - free living nematodes - soil ecology - identification - molecular ecology - soil monitoring

    Soil performs numerous functions, which allow us to produce food and feed and provide us with clean freshwater. These functions rely on the high diversity of organisms residing in soils. Within the high complexity of the soil food web, nematodes, worm-shaped animals belonging to the phylum Nematoda, are an informative group for assessing the status of a soil-dwelling community due to their ubiquity, abundance and trophic diversity. Although nematodes also possess several other assets favourable for a biological indicator of soil ecosystems (e.g. easy extractability, differential sensitivities to disturbances, ecological interpretability), their microscopic identification demands a considerable amount of expertise and time because of their relatively conserved morphology. Hence, the use of a molecular method for the identification and quantification of nematode assemblages has the potential to lift practical limitations and allows for more intensive sampling schemes. The aim of the research described in this thesis was to assess the suitability of molecular taxon-specific assays, developed on the basis of a phylum-wide molecular framework of 2,400 full-length small subunit ribosomal DNA sequences, for the monitoring of nematode assemblages in field experiments. The method was applied to monitor the impact of different types of disturbances on the soil food web, i.e. agricultural practices, invasive plant species and the effects of genetically modified crop (potato).

    The second chapter of this thesis presents the background of the molecular method and the results of its first field application. It demonstrates the suitability of this method for use in extensive field experiments and the results of this study reveal distinct seasonal fluctuations between nematode genera classified to belong to the same feeding type group. A distinct response of nematode genera within trophic groups – taxonomically diverse groups of nematodes having the nature of their main food source as a common denominator – was also observed in the study described in Chapter 3. In this chapter, a study was conducted to investigate the impact of an invasive plant species called Giant goldenrod (Solidago gigantea, native to North America) on the plant community as well as on different trophic levels of the soil food web. In addition to monitoring the nematode community, pH and fungal biomass were measured in plots invaded or uninvaded by Giant goldenrod in two contrasting habitats. The results revealed that, in addition to outcompeting native plant species, this invader also reduced pH and increased fungal biomass in the soil of both habitats. Based on the results concerning the nematode community, the impact on the soil food web seemed to be selective since the local increase of fungal biomass appeared to benefit only one fungivorous nematode lineage of the three present in the field. This suggests that invasion by Giant goldenrod only stimulates one part of the fungal community.

    Contrary to the preceding chapters, the effects of different disturbances on the nematode community were studied in an arable setting in chapters 4 and 5. Chapter 4 describes a field experiment in which the impact of biofumigation, a pest control measure, on the nematode community was assessed. Biofumigation is considered as an alternative for the use of synthetic fumigants and entails the incorporation of mulched brassicaceous plant material, which, upon de-compartmentalisation, releases general biocides called isothiocyanates. In our experiment, these compounds as well as their precursors could not be related to the effects observed for the nematode community. Therefore, changes in nematode assemblages are more likely to be related to the intense mechanical disturbance and green manure – the addition of a large quantity of fresh plant material to the topsoil – rather than the release of isothiocyanates from the plant material

    Chapter 5 presents a field experiment in which the possible belowground side effects of a waxy starch GM potato, a genetically modified plant blocked in its amylose biosynthesis, were investigated. The nematode community was monitored during the growing season of this GM variety, its parental line and four other conventional potato cultivars in two experimental fields. Although we observed clear effects of location and time, no GM-related effects were observed on the nematode community. Our results, in line with previous studies concerning the microbial community, indicate there are no observable, non-transient effects related to this particular GM trait on the soil food web during the growing season.

    Overall, the results presented in this thesis demonstrate that, first of all, the developed molecular approach is suitable as a tool for the quantitative monitoring of nematode assemblages in field experiments, and, secondly, how a molecular monitoring method based on nematode taxon-specific DNA motifs can be exploited to get new insights into the ecology of terrestrial nematodes and – more in general – into the ecological functioning of this obscure, highly biodiverse and poorly understood habitat below our feet.

    Characterization and epidemiology of members of the genus Torradovirus
    Verbeek, M. - \ 2013
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): Rene van der Vlugt; Richard Kormelink. - S.l. : s.n. - ISBN 9789461736703 - 159
    solanum lycopersicum - tomaten - plantenvirussen - picornaviridae - identificatie - epidemiologie - spanje - solanum lycopersicum - tomatoes - plant viruses - picornaviridae - identification - epidemiology - spain

    The research described in this thesis focuses on the molecular and biological characterization of a new group of plant viruses. At the start of this research only a ‘torrado’ disease in tomato was known, which is recognised by necrosis on leaves and fruits, that eventually turn into its typical and devastating burnt-like symptoms. Using a wide range of available (virological) tools the causal agent was identified as a so-far unknown spherical virus of approximately 28 nm in diameter. Further analysis revealed that the virus contained a bi-partite RNA genome of which the entire nucleotide sequence was elucidated. The virus was named after the Spanish name of the disease, hence Tomato torrado virus (ToTV). Although this virus has been found mainly in Europe, it is emerging and meanwhile found in Central America and Australia.

    After the discovery of ToTV, another disease suspected to be caused by a torrado-like virus was analysed. It was shown that this disease, which was found in tomatoes grown in Mexico, was caused by a similar but distinct torradovirus named Tomato marchitez virus (ToMarV). Its molecular and biological features, as analysed and described in this thesis, supported the proposal of a new genus denoted Torradovirus, named after its first representative. This genus was recognized and classified by the International Committee on Taxonomy of Viruses (ICTV) into the family Secoviridae (order Picornavirales). Currently, the genus Torradovirus harbours, besides the recognised species ToTV and ToMarV, also the tentative species Tomato chocolàte virus (ToChV), Tomato chocolate spot virus (ToChSV, analysed by another research group), and Lettuce necrotic leaf curl virus (LNLCV).

    Elucidation of torradovirus genome sequences revealed that their RNA1 contained one open reading frame (ORF) that contains motifs typical for proteins involved in replication, i.e. helicase, protease and RNA-dependent RNA polymerase (RdRp). RNA2, on the other hand, contained two ORFs (RNA2-ORF1 and RNA2-ORF2) that coded for a small (~20 kDa) protein of unknown function, the putative movement protein, and the three coat proteins, respectively.

    Considering the economic importance of torradoviruses and their emerging character, attempts were made to develop a diagnostic tool to detect the presence of these viruses. To this end generic PCR primer pairs (Torradovirus-1F/Torradovirus-1R and Torradovirus-2F/Torradovirus-2R) were developed against highly conserved regions in RNA1 and RNA2, respectively. Evaluation of these primer sets revealed that they supported detection of all currently known torradoviruses.

    Limited information indicated that members of the genus Torradovirus were transmitted by whiteflies. By a detailed study using varying acquisition access periods and inoculation access periods, it was demonstrated that ToTV, ToMarV and ToChV are all transmitted by three whitefly species, namely Trialeurodes vaporariorum, Trialeurodes abutilonea and Bemisia tabaci. The mode of transmission was determined as semi-persistent, i.e. like viruses that enter and remain in the foregut until being transmitted to another plant host. However, localisation of the viral RNA within the whitefly vector confirmed the presence of virus in the stylets and thereby showed that torradoviruses represent the first spherical viruses transmitted by whiteflies in a semi-persistent and stylet-borne manner.

    Species identification workshops 2012 and 2013: Gobies and Elasmobranchs
    Boois, I.J. de; Bolle, L.J. - \ 2013
    IJmuiden : IMARES (Report / IMARES Wageningen UR 13.009) - 16
    demersale visserij - elasmobranchii - pomatomidae - aquatische ecosystemen - identificatie - benthos - demersale vissen - demersal fisheries - elasmobranchii - pomatomidae - aquatic ecosystems - identification - benthos - demersal fishes
    Up until now, gobies of the genus Pomatoschistus have not been identified to the lowest taxonomic level during The Demersal Fish Survey (DFS), Sole Net Survey (SNS) and Beam Trawl Survey (BTS). It is however an abundant genus in the catches in the shallow coastal zone stations and it can be assumed that the species play a role in the coastal ecosystem. The correct identification on board is however questionable. For that reason, during the 2012 DFS extra attention has been paid to identification of Pomatoschistus species. On each of the three vessels carrying out the DFS, a Pomatoschistus expert (Cindy van Damme or Bram Couperus) was taken on board for one week. On board Stern and Schollevaar all Pomatoschistus have been identified to the species, and on board Isis part of the specimens were identified to the species, and part was taken to the lab. Samples were frozen following a protocol to keep the quality of the fish as good as possible and were taken back to the lab for identification. Main problems arose in identification of P. lozanoi and P. minutus. As even the experts did not agree, it is proposed to treat P. lozanoi and P. minutus as a group of species, and to identify the other species to the species level. From identification workshops and tests on demersal fish and benthos it became clear that specific attention should be paid to the elasmobranch species. On 20 March 2013 a dedicated species identification workshop focusing on elasmobranch species was organised for IMARES employees. Main purpose of the workshop was quality assurance of species identification of elasmobranch species. IMARES projects influenced by the quality of this species identification are i.a. the seagoing statutory task surveys, statutory task discard projects, PULSMON. The species to be identified were collected during the BTS2011 and BTS 2012 and stored in the freezer. Results are presented by expertise level of the employees. The expertise level was based on expertise and responsibilities during surveys and discard sampling. The results of the test and workshop were in line with earlier workshops focusing on fish and macrobenthos.
    Loofbomen in Nederland en Vlaanderen : soorten en hybriden
    Goudzwaard, L. - \ 2013
    Zeist : KNNV - ISBN 9789050114325 - 432
    loofhout - bosbomen - bomen - soorten - identificatie - foto's - habitus - vlaanderen - nederland - taxonomie - broadleaves - forest trees - trees - species - identification - photographs - habit - flanders - netherlands - taxonomy
    Loofbomen van Nederland en Vlaanderen beschrijft 268 verschillende boomsoorten en hybriden en 400 verschillende variëteiten waaronder tal van boomgeslachten, zoals Acer (esdoorn), Fagus (beuk), Magnolia, Malus (appel) en Quercus (eik), maar ook minder bekende boomsoorten, zoals venkelhout (Sassafras albidum) en lederboom (Ptelea trifoliata).H erkenning, gebruik en ziektegevoeligheid komen aan bod, maar ook de geschiedenis van het boomgeslacht en de plaatsen waar prachtige exemplaren van de soort te zien zijn. In dit boek leest u waar u complete collecties van boomgeslachten kunt bekijken, evenals monumentale bomen.
    Unieke perceelcodering = Unique identification of agricultural fields
    Goense, D. - \ 2012
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 667) - 46
    precisielandbouw - geografische informatiesystemen - perceelsvorm (landbouwkundig) - iso - identificatie - teeltsystemen - akkerbouw - precision agriculture - geographical information systems - field shape - iso - identification - cropping systems - arable farming
    An identifier is specified for the global unique identification of agricultural fields. Different categories of fields are defined. Requirements for the identifier are formulated together with stakeholders. After inventory of systems for unique identification it was concluded that an identifier based on ISO15459is most suited to fulfil the requirements.
    Fluorescentievingerafdruk van Aardappel, Melganzenvoet en Mais : Eerste resultaten van plantonderscheid met behulp van fluorescentie
    Groot, T.T. ; Nieuwenhuizen, A.T. - \ 2012
    Wageningen : Plant Research International - 25
    akkerbouw - veldgewassen - precisielandbouw - multispectrale beelden - beeldanalyse - beeldverwerking - identificatie - informatieverwerking - onkruiden - gewassen - arable farming - field crops - precision agriculture - multispectral imagery - image analysis - image processing - identification - information processing - weeds - crops
    Als het spectrum van één “soort” (gewas) vergeleken wordt met de rest (onkruid) neemt het onderscheid van het “gewas” af tot 70%. Het lijkt dus nodig ook de spectra van alle soorten onkruid in het veld te kennen om een goed onderscheid mogelijk te maken. De doelstelling voor deze metingen is een onderscheid tussen de planten met 95% betrouwbaarheid te kunnen maken.
    Short ID sheet whales and dolphins Dutch Caribbean
    Scheidat, M. ; Geelhoed, S.C.V. - \ 2012
    IJmuiden : IMARES (Report / IMARES Wageningen UR C022/14) - 8
    walvissen - dolfijnen - identificatie - dieridentificatie - caribische zee - whales - dolphins - identification - animal identification - caribbean sea
    Identification sheet whales and dolphins Dutch Caribbean.
    Gedifferentieerd diergezondheidsbeleid : case studie Weideschapen
    Hagenaars, T.H.J. ; Asseldonk, Marcel van; Bontje, D.M. ; Puister-Jansen, L.F. ; Backer, J.A. ; Nodelijk, G. ; Bergevoet, R.H.M. - \ 2012
    Lelystad : Central Veterinary Institute (CVI rapport / Central Veterinary Institute, 13/CVI0182 ) - 40
    schapenhouderij - mond- en klauwzeer - schapenziekten - ziekteoverdracht - identificatie - registratie - regelingen - verspreide infecties - gelderse vallei - Nederland - sheep farming - foot and mouth disease - sheep diseases - disease transmission - identification - registration - regulations - disseminated infections - gelderse vallei - Netherlands
    De vraagstelling voor deze studie luidt: in welke mate neemt het risico op verspreiding van Mond-en-Klauwzeer toe als de huidige Regeling Preventie, bestrijding en monitoring van besmettelijke dierziekten en zoönosen en TSE’s (Regeling preventie) zodanig zou worden aangepast dat schapen vanaf een verzamelcentrum naar een weidebedrijf vervoerd mogen worden? Vervolgens bestaat de aanpak van deze studie uit de volgende onderdelen: - studie van de huidige verplaatsingen zoals gemeld in Identificatie & Registratie (I&R); - interviews met deskundigen; - epidemiologische risicoberekeningen; - economische analyse van de directe kosten; - gevoeligheidsanalyse van de uitkomsten voor (parameter)onzekerheden. De berekeningen richten zich op het scenario dat insleep van MKZ in Nederland op een schapenbedrijf plaatsvindt dat is gelegen in de Gelderse Vallei. De focus ligt hierbij op het percentage waarmee het risico van MKZ-verspreiding zou veranderen na aanpassing van de Regeling preventie.
    Kwaliteit en ruimtelijke data in relatie tot het LPIS : kwaliteitsaspecten rondom het beheer van ruimtelijk data
    Meijer, M. ; Vullings, L.A.E. - \ 2012
    Wageningen : Alterra (Alterra-rapport 2285) - 142
    verkaveling - identificatie - registratie - databanken - gemeenschappelijk landbouwbeleid - kwaliteitsnormen - land parcelling - identification - registration - databases - cap - quality standards
    Elke lidstaat is verplicht om een Geïntegreerd Beheers- en Controlesysteem (GBCS) op te zetten. Een belangrijk onderdeel van dit GBCS is een systeem voor de identificatie van percelen landbouwgrond, ook wel perceelsregister of LPIS (Land Parcel Identification System) genoemd. In 2010 is door de EU een nieuw raamwerk opgezet om die kwaliteit van het perceelsregister te toetsen. Dit raamwerk wordt ook wel LPIS QAF genoemd. De elementen die deel uitmaken van dit kwaliteitsraamwerk komen voor een groot deel overeen met al bestaande kwaliteitsraamwerken zoals ISO en NEN. De uitkomsten van het LPIS QAF geven over het algemeen een goed beeld van de kwaliteit van het perceelsregister, zij het dat een aantal elementen sterk context afhankelijk zijn.
    Starch identification supported by expert system determinator
    Raamsdonk, L.W.D. van; Hekman, W.E. ; Pinckaers, V.G.Z. ; Vliege, J.J.M. ; Ruth, S.M. van - \ 2012
    zetmeel - gemodificeerd zetmeel - identificatie - voedselanalyse - starch - modified starches - identification - food analysis
    Identification of starch as ingredient is important for a range of purposes. The Starch Identification System as implemented in the platform Determinator is helpful in this respect since it allows consistent identification of starch in a large variety of products.
    Voersysteem voor het individueel voeren van vleesvarkens: 'Voeren op maat' : de ontwikkeling van een nieuw voersysteem binnen project 'Vitale vleesvarkens'
    Dirx-Kuijken, N.C.P.M.M. ; Peet-Schwering, C.M.C. van der; Hoofs, A.I.J. - \ 2012
    Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 600) - 18
    varkenshouderij - vleesproductie - varkensvoeding - voedersystemen - individuele voeding - identificatie - individuele kenmerken - pig farming - meat production - pig feeding - feeding systems - individual feeding - identification - individual characteristics
    Om het resultaat van vleesvarkens te verhogen, is een ontwikkeltraject in gang gezet voor het voersysteem 'Voeren op maat'. Hiermee kunnen vleesvarkens individueel gevoerd worden op basis van individuele dierherkenning. In dit ontwikkeltraject is het systeem beoordeeld op de vooraf gestelde eisen.
    Systematics of the blackfly subgenus Trichodagmia Enderlein (Diptera: Simuliidae: Simulium) in the new world
    Hernández Triana, L.M. - \ 2011
    Wageningen University. Promotor(en): Marc Sosef; R.J. Post. - s.n. - ISBN 9789085858652 - 536
    simulium - taxonomy - identification - keys - nearctic region - simulium - taxonomie - identificatie - determinatietabellen - nearctisch gebied

    Systematics of the blackfly subgenus Trichodagmia ENDERLEIN (Diptera: Simuliidae:

    Simulium) in the New World

    The systematics of the New World subgenus Trichodagmia has been reassessed by employing an

    integrated taxonomic approach based upon revisionary taxonomy, phylogenetic (cladistics) analysis, and

    DNA barcoding. This subgenus included several species of great medical importance, which are all

    morphologically very similar. The history of the taxonomy and classification of the subgenus

    Trichodagmia has been put into context with other subgenera within New World Simuliidae, while

    descriptions and keys to the identification of species in this subgenus are also given.

    The subgenus Obuchovia is here considered a new junior synonym of Trichodagmia, and all its

    constituents’ species are now placed in the ALBELLUM species group to represent a Palaearctic

    element within this subgenus. Three new junior synonymies are here proposed: Simulium chiriquiense

    FIELD is a synonym of S. ethelae DALMAT n. syn.; S. biuxinisa COSCARÓN & IBÁÑEZ-BERNAL is a

    synonym of S. paynei VARGAS n. syn.; and S. keenani FIELD is a synonym of S. earlei VARGAS, MARTÍNEZ

    PALÁCIOS &DÍAZ NÁJERA n. syn. A neotype is designated for S. lahillei (PATERSON & SHANNON) and a

    lectotype for S. pulverulentum KNAB.1 Simulium falculatum ENDERLEIN is transferred from the

    TARSATUM species group of to the CANADENSE species group based on the morphology of the

    female genitalia. Two species, S. rivasi RAMÍREZ PÉREZ and S. oviedoi RAMÍREZ PÉREZ, are transferred

    from the TARSATUM species group to the subgenus Psilopelmia based on the morphology of the male

    gonostyle and the ventral plate. Keys to separate all species groups and species based on the adults,

    pupae and larvae are also provided.

    The phylogeny and classification of the subgenus Trichodagmia is delineated using a cladistic

    analysis of 63 taxa based on males, females, pupae and larvae, including two species belonging to the

    subgenus Aspathia and two species of the subgenus Simulium s.str. that served as outgroups. Analysis of

    the original full data set [67 taxa and 67 characters] with multistate characters treated as unordered

    under equal weights led to poorly resolved trees, with many polytomies within TARSATUM [= old

    subgenus Hemicnetha] and CANADENSE [= old subgenus Hearlea]. Nonetheless, the ALBELLUM [=

    old subgenus Obuchovia] and PICTIPES [= old subgenus Shewellomyia] species groups, and some clades

    within the CANADENSE species group were well supported. In the most parsimonious cladograms,

    the position of S. falculatum was problematic as it was placed basal to Trichodagmia. The position of S.

    jeteri, albeit within the ORBITALE [= old subgenera Trichodagmia + Thyrsopelma of MIRANDA-ESQUIVEL

    & COSCARÓN, 2001] clade, was also poorly resolved. This was certainly due to the numerous missing

    data in these two taxa. Therefore, they were removed from the data set together with other taxa in

    which three life stages (> 70% of characters) were missing (e.g. S. paracarolinae and S. tarsale). A second

    analysis was then performed with 63 taxa and 67 characters. In this analysis, the Strict Consensus Tree

    was better resolved and certain clades within the expanded concept of Trichodagmia (sensu SHELLEY et al.,

    2010) were recovered as monophyletic with high support values. The ALBELLUM species group is

    monophyletic in a sister-group relationship with the other species groups in Trichodagmia (sensu SHELLEY

    et al., 2010). The ORBITALE species group clade was recovered as monophyletic by a unique

    combination of seven characters with 89% bootstrap support. In this clade, all species close to S.

    guianense s.l. were better diagnosed by a combination of four characters, one of which (male ventral plate

    with a globular median process) was unique to this group. The position of S. hirtipupa is better resolved

    in the latter clade by the presence of black spiniform setae in the frontoclypeus and thorax of the pupa.

    In contrast, the TARSATUM and CANADENSE species groups were diagnosed by only four

    and five characters, respectively. Within the CANADENSE species group only species with larvae

    having sclerotized plates in the posterior region of the abdomen were well resolved. Species in the

    TARSATUM group were homoplastic. The PICTIPES group is only diagnosed by homoplasies, but the

    combination of these characters is unique to this clade (polythetic taxon). In general, this study supports

    some of the taxonomic changes proposed in SHELLEY et al. (2010), in which the subgeneric-names

    Hearlea, Hemicnetha, Shewellomyia, Trichodagmia + Thyrsopelma (sensu MIRANDA-ESQUIVEL & COSCARÓN,

    502

    2001) are treated as species groups within the subgenus Trichodagmia. Moreover, this study also supports

    the proposal of Obuchovia as a junior synonym within the clade Trichodagmia to represent the

    ALBELLUM species group.

    The utility of the COI DNA barcoding methodology for identification of species in the subgenus

    Trichodagmia and related taxa has been tested. In total, 24 morphospecies within the current expanded

    morphological concept of Trichodagmia were analyzed. In addition, three species of the subgenus

    Aspathia and 10 species of the subgenus Simulium s.str. were also included in the analysis because of their

    putative phylogenetic relationship with Trichodagmia. Within the barcoding neighbour-joining tree, most

    of the specimens were grouped together according to morpho-taxon (species groups and species).

    Mean genetic distance amongst groups (morphospecies) averaged 11.2% (ranged 2.8-19.5%), whereas

    intraspecific genetic divergence within morphologically distinct species averaged 0.5% (range 0-1.3%).

    In known species complexes, maximum values of genetic divergence (3.28-3.79%) indicate the probable

    presence of cryptic diversity. DNA barcoding achieved nearly 100% success in identifying all specimens

    of the subgenus Trichodagmia and related taxa.

    The existence of well defined groups within S. piperi, S. duodenicornium, S. canadense and S. rostratum

    highlighted the possible presence of species complexes in these taxa. In addition, the suspected

    presence of a sibling species in S. paynei and S. tarsatum among populations of Belize, Costa Rica, and

    the USA is confirmed. The use of shorter barcodes (midi and minibarcodes) from specimens held in

    collections was problematic with regards to the DNA quality and PCR success. However, in the cases

    that a readable sequence was obtained, they were sufficient for reliable species identification. With

    regards to the different extraction and preservation techniques tested, larvae preserved in diluted

    Carnoy’s (10% acetic acid) provided full DNA barcodes. Furthermore, legs added directly to the PCR

    mix from freshly collected individuals provided full length barcodes sequences. However, specimens of

    more than 10 years old did not yield good PCR products. In short, I conclude that DNA barcoding in

    combination with a morphological benchwork platform is an effective approach for identification and

    delineation of species in the subgenus Trichodagmia, and the discovery of hidden diversity in this taxon. 

    Determinator datamodel Jacobskruiskruid, versie 3.0 NL
    RIKILT, - \ 2011
    RIKILT
    senecio jacobaea - ruwvoer (forage) - giftige planten - senecio - modellen - identificatie - senecio jacobaea - forage - poisonous plants - senecio - models - identification
    Het voorkomen en zeker de uitbreiding in areaal van jacobskruiskruid (Senecio jacobaea, of bekend onder de nieuwere naam Jacobaea vulgaris) is een bedreiging voor de veestapel in Nederland. Het is gewenst om in weilanden en bij de productie en verwerking van ruwvoeder tijdig risico’s in te schatten. Een extra factor hierbij is dat niet alleen jacobskruiskruid, maar ook andere soorten van het geslacht kruiskruid dezelfde giftige stoffen bevatten. Met name de soorten klein kruiskruid en bezemkruiskruid hebben een uitgebreide verspreiding in Nederland of komen in toenemende mate voor, maar worden niet altijd als risicofactor herkend. Het programma Determinator in combinatie met het datamodel Jacobskruiskruid is bedoeld om gebruikers, weg- en terreinbeheerders en andere betrokkenen in de productieketen van ruwvoeder (met name grasproducten) te ondersteunen bij het herkennen van kruiskruid, en de kruiskruidsoorten te onderscheiden van andere geelbloeiende planten. Door een juiste herkenning kan een verantwoorde keuze gemaakt worden om partijen gras of andere ruwe producten te gebruiken als ruwvoeder of op andere wijze af te voeren en te gebruiken.
    Report of the Workshop on the identification of clupeoid, flatfish, gadoids and other fish larvae (WKIDFL)
    Imares, - \ 2011
    IJmuiden : IMARES (ICES WKIDFL report 2011)
    conferenties - larven - vis - dieridentificatiesystemen - dieridentificatie - identificatie - overeenkomsten - pleuronectiformes - conferences - larvae - fish - animal identification systems - animal identification - identification - agreements - pleuronectiformes
    The Workshop on the Identification of clupeoid, flatfish, gadoid and other fish larvae (WKIDFL) met from 5 to 9 September 2011 in IJmuiden, The Netherlands, to calibrate fish larvae identification. The meeting was chaired by Cindy van Damme, The Neth-erlands, and Matthias Kloppmann, Germany. In total 17 persons representing 10 in-stitutes from 8 countries participated in the workshop. The majority of the time at the workshop was spent identifying fish larvae. The re-sults promoted discussion and highlighted specific problem areas. These discussions led to the further development of standard keys and larval identification characteris-tic tables.
    Focus op landschap, Herfotografie als instrument voor landschapsmonitoring
    Kruit, Jeroen ; Veer, P.M. - \ 2011
    landscape - identification - photography - registration
    Emissieregistratie van landbouwbedrijven : verbeteringen met behulp van het Geografisch Informatiesysteem Agrarische Bedrijven
    Os, J. van; Gies, T.J.A. ; Naeff, H.S.D. ; Jeurissen, L.J.J. - \ 2011
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-werkdocument 275) - 72
    dierhouderij - statistische gegevens - landbouwstatistieken - dierlijke meststoffen - ammoniakemissie - identificatie - registratie - regio's - animal husbandry - statistical data - agricultural statistics - animal manures - ammonia emission - identification - registration - regions
    Voor het berekenen van emissie door de Emissieregistratie in Nederland werd tot nu toe gebruik gemaakt van gegevens uit de Landbouwtelling. Hierin wordt jaarlijks per bedrijf opgevraagd hoeveel dieren er aanwezig zijn. Sommige bedrijven houden echter een deel van het vee op nevenvestigingen. Via diertellingen vanuit de Identificatie en Registratie van landbouwhuisdieren zijn de nevenvestigingen gelokaliseerd en gekoppeld aan de hoofdvestigingen. Hiermee kunnen de dieren van de landbouwtelling aan de juiste locatie gekoppeld worden, waardoor de Emissieregistratie tot een betere ruimtelijke verdeling van bijvoorbeeld de ammoniakuitstoot uit de veehouderijbedrijven kan komen. Deze herverdeling van dieren is uitgevoerd met de landbouwtelling van 2009, waarbij een koppeling is gemaakt met de staltypen van 2008.
    Barcode van DNA. Democratisering van de taxonomie door digitaal identificatiesysteem
    Bakker, F.T. - \ 2011
    Kunst en Wetenschap 2011 (2011)1. - ISSN 0927-3506 - p. 15 - 16.
    taxonomie - biodiversiteit - genexpressieanalyse - dna - genoomannotatie - identificatie - taxonomy - biodiversity - genomics - genome annotation - identification
    Het herkennen van biologische soorten aan de hand van een gestandaardiseerde DNA-barcode heeft de laatste tijd een enorme vlucht genomen. Gedreven door aan de ene kant de biodiversiteitscrises en de mogelijke global change, en aan de andere kant zowel razendsnelle technologische vooruitgang als ook het vooruitzicht dat niet genoeg klassieke taxonomen worden opgeleid voor de nabije toekomst, lijkt DNA-barcoding zich een strategische plek te veroveren op huidige, al dan niet toegepaste, biodiversiteitsonderzoeksagenda’s. Maar er is meer en er blijven bovendien nog genoeg vragen over.
    Grip op virussen
    Vlugt, R.A.A. van der; Verbeek, M. ; Roenhorst, A. ; Botermans, M. ; Kock, M.J.D. de; Schadewijk, T. van; Miglino, R. ; Kormelink, R. ; Lent, J.W.M. van - \ 2011
    Gewasbescherming 42 (2011)2. - ISSN 0166-6495 - p. 62 - 65.
    virologie - plantenvirussen - detectie - identificatie - databanken - viroïden - epidemiologie - phytoplasma - virology - plant viruses - detection - identification - databases - viroids - epidemiology - phytoplasma
    Aan het begin van het FES-project ‘Versterking infrastructuur plantgezondheid' zijn de belangrijkste knelpunten op plantenvirologisch gebied in Nederland geïnventariseerd. Criteria hierbij waren vooral fytosanitaire status, economisch belang en de behoefte aan betrouwbare detectie- en identificatiemethoden. Op basis hiervan is een prioriteitenlijst opgesteld van de (gereguleerde) virussen uit de volgende virusgroepen: Potyvirussen, Nepovirussen, Tospovirussen en Potexvirussen. Daarnaast werd zo’n lijst opgesteld voor viroïden en fytoplasma’s. Aan de prioriteitenlijst werden toegevoegd: Pospiviroïden en Fytoplasma’s. De verkregen gegevens werden opgenomen in de Q-bank.
    Taxonomie van plant-pathogene schimmels als basis voor identificatie en detectie: resultaten van het Uitvoeringsconsortium Schimmels
    Zwiers, L.H. ; Aveskamp, M.M. ; Bonants, P.J.M. ; Brouwer, H. ; Cock, A. de; Damm, U. ; Gruyter, H. de; Meekes, E. ; Verstappen, E.C.P. ; Woudenberg, J. - \ 2011
    Gewasbescherming 43 (2011)2. - ISSN 0166-6495 - p. 57 - 62.
    mycologie - schimmels - plantenziekteverwekkende schimmels - databanken - colletotrichum - phoma - phytophthora - identificatie - mycology - fungi - plant pathogenic fungi - databases - colletotrichum - phoma - phytophthora - identification
    Plant-pathogene schimmels worden traditioneel geïdentificeerd op basis van morfologische karakteristieken. Dit is over het algemeen tijdrovend, veel expertise en leidt vaak tot misidentificatie. Het doel van het werk uitgevoerd door het Uitvoeringsconsortium Schimmels was dan ook gericht op de verbetering van detectie- en identificatietechnieken van plant pathogene schimmels met de nadruk op quarantaineorganismen. Op grond van het economische, wetenschappelijke, en ecologische belang, de aanwezigheid van Q-organismen, en de wetenschappelijke startpositie binnen Nederland is in eerste instantie de keuze gevallen op de geslachten Colletotrichum, Phoma, en Phytophthora. De gegenereerde dat zijn opgenomen in de Q-bank.
    Koudmerken : actualisatie van het gebruik van koudmerken op Nederlandse melkveebedrijven
    Hopster, H. ; Zijlstra, J.T. - \ 2011
    Leeuwarden : Hogeschool Van Hall Larenstein, Lectoraat Welzijn van Dieren - 15
    dierhouderij - melkveehouderij - identificatie - merken - brandmerken - bevriezing - dierenwelzijn - diergezondheid - animal husbandry - dairy farming - identification - marking - branding - frostbite - animal welfare - animal health
    Voor identificatie van runderen zijn wettelijk 2 ingrepen toegestaan. De 2 wettelijk verplichte gele oornummers laten daarmee geen ruimte voor het aanbrengen van een koudmerk. Op dit moment heeft de rundveesector van het ministerie van Economische zaken, Landbouw en Innovatie een ontheffing van dit verbod op het gebruik van koudmerken als derde ingreep. Deze ontheffing loopt in juni 2011 af. Dit rapport biedt inzicht in de acute, de subacute en de chronische effecten van koudmerken op het welzijn van de koe. Daarnaast is bij een aselecte en representatieve groep van 285 melkveehouders een telefonische enquête uitgevoerd naar het gebruik van koudmerken, gekoppeld aan bedrijfskenmerken. Koudmerken als ingreep brengt bij runderen een acute stressrespons teweeg. Uit de fysiologische- en gedragsreacties kan echter niet worden afgeleid of er ernstige schade aan het welzijn en de gezondheid van runderen wordt toegebracht.
    RFID biedt ook perspectief voor laanbomen
    Baltissen, A.H.M.C. ; Sluis, B.J. van der - \ 2011
    De Boomkwekerij 24 (2011)2. - ISSN 0923-2443 - p. 12 - 13.
    elektrotechniek - rfid - elektronica - identificatie - boomkwekerijen - straatbomen - electrical engineering - rfid - electronics - identification - forest nurseries - street trees
    Binnenkort zijn CC-karren elektronisch te registreren met RFID (Radio Frequency Identification) en deze technologie biedt ook mogelijkheden voor de laanbomenketen. Uit onderzoek door PPO blijkt dat zowel de kweker als de klant voordeel kan behalen met RFID. Er zijn echter nog veel praktische vragen te beantwoorden.
    Some mossmites new for the Netherlands (Acari: Oribatida)
    Siepel, H. ; Dimmers, W.J. - \ 2010
    Nederlandse Faunistische Mededelingen 34 (2010). - ISSN 0169-2453 - p. 41 - 44.
    mijten - oribatida - identificatie - soorten - inventarisaties - mites - oribatida - identification - species - inventories
    Bestudering van materiaal uit enkele Alterra projecten leverde negen soorten mosmijten op die nog niet waren opgenomen in de recent gepubliceerde Nederlandse naamlijst. Het totaal aantal soorten voor Nederland komt hiermee op 327.
    Anthericaceae, Burmanniaceae, Colchiceae, Crassulaceae, Dipterocarpaceae, Lemnaceae, Pittosporaceae, Rosaceae, Ternstroemiaceae, Thismiaceae, Triuridaceae
    Sosef, M.S.M. ; Florence, J. ; Ngok Banak, L. ; Bourobou Bourobou, H.P. - \ 2010
    Weikersheim [etc.] : Margraf [etc.] (Flore du Gabon 41) - ISBN 9783823615972 - 75
    planten - taxonomie - identificatie - determinatietabellen - gabon - plants - taxonomy - identification - keys - gabon
    Apodanthaceae, Balanophoraceae, Campanulaceae, Caricaceae, Hyacinthaceae, Hydroleaceae, Lobeliaceae, Menyanthaceae, Nymphaeaceae, Pontederiaceae, Typhaceae
    Sosef, M.S.M. ; Florence, J. ; Ngok Banak, L. ; Bourobou Bourobou, H.P. - \ 2010
    Weikersheim [etc.] : Margraf [etc.] (Flore du Gabon 40) - ISBN 9783823615835 - 73
    planten - taxonomie - identificatie - determinatietabellen - gabon - plants - taxonomy - identification - keys - gabon
    Aardkastanje, onopvallend en te weinig om te eten
    Spruijt, T. - \ 2010
    Nature Today 2010 (2010)05-07.
    bunium bulbocastanum - apiaceae - wilde planten - karakteristieken - identificatie - duinen - noord-holland - bunium bulbocastanum - apiaceae - wild plants - characteristics - identification - dunes - noord-holland
    Hij staat vanaf half juni volop in bloei, maar wordt door weinigen gezien. Hoewel een zoektocht op Google anders doet vermoeden, wordt hij niet meer gegeten. De Aardkastanje is daarvoor te onopvallend en te zeldzaam in Nederland. Toch is het een bijzondere schermbloem.
    Multiplex-detectie van Phytophthora: "padlock-based Universal Multiplex detection Array" (pUMA)
    Gaszczyk, K. ; Mendes, O. ; Verstappen, E.C.P. ; Bonants, P.J.M. ; Schoen, C.D. - \ 2010
    Gewasbescherming 41 (2010)3. - ISSN 0166-6495 - p. 145 - 146.
    phytophthora - detectie - identificatie - biochemische technieken - nucleotidenvolgordes - polymerase-kettingreactie - phytophthora - detection - identification - biochemical techniques - nucleotide sequences - polymerase chain reaction
    Plant Research International heeft een diagnostische methode ontwikkeld die toe te passen is 'in planta', en ook de meest recent beschreven (quarantaine-) soorten omvat. De methode omvat de ontwikkeling van een generieke Phytophthora-methode gevolgd door een Phytophthora-identificatie.
    Identification and epidemiology of pospiviroids
    Verhoeven, J.Th.J. - \ 2010
    Wageningen University. Promotor(en): Just Vlak, co-promotor(en): J.W. Roenhorst. - [S.l. : S.n. - ISBN 9789085856238 - 136
    solanum tuberosum - aardappelen - solanum lycopersicum - tomaten - viroïden - aardappelspindelknolviroïde - detectie - identificatie - methodologie - epidemiologie - siergewassen - waardplanten - moleculaire detectie - solanum tuberosum - potatoes - solanum lycopersicum - tomatoes - viroids - potato spindle tuber viroid - detection - identification - methodology - epidemiology - ornamental crops - host plants - molecular detection
    Pospiviroids can cause serious diseases in potato and tomato. Since 1988 viroid infections have occasionally been detected in tomato crops in the Netherlands. To identify these viroid isolates unequivocally, two novel universal primer sets were designed for ‘Reverse Transcription-Polymerase Chain Reaction’ (RT-PCR), a sensitive technique enabling detection and identification of pospiviroids. Sequence analyses identified the viroids as Citrus exocortis viroid (CEVd), Columnea latent viroid (CLVd) and Potato spindle tuber viroid (PSTVd). To find potential sources of infection, ornamental plants were screened for the presence of pospiviroids. These surveys revealed many new pospiviroid host plants as well as high infection rates for PSTVd in some ornamental species. Phylogenetic studies provided evidence that the PSTVd isolates from tomato originated from vegetatively propagated, solanaceous host plants. This conclusion was further substantiated by showing a high stability of predominant pospiviroid genotypes after mechanical pospiviroid transmission from ornamentals to potato and tomato. In addition, several experiments showed that mechanical inoculation is a likely way of pospiviroid transmission between these crops. In addition, a new pospiviroid from pepper was characterized, i.e. Pepper chat fruit viroid that also can infect potato and tomato. The results of above findings on pospiviroids are discussed in a broader context addressing diagnostic and epidemiological aspects as well as risk assessment in relation to quarantine measures.
    Highlights of the Didymellaceae: a polyphasic approach to characterise Phoma and related pleosporalean genera
    Aveskamp, M.M. ; Gruyter, H. de; Woudenberg, J. ; Verkley, G. ; Crous, P.W. - \ 2010
    Utrecht : CBS Fungal Biodiversity Centre (Studies in mycology 65) - ISBN 9789070351793 - 65
    dothideales - phoma - taxonomie - fylogenie - identificatie - pleosporaceae - coelomycetes - dothideales - phoma - taxonomy - phylogeny - identification - pleosporaceae - coelomycetes
    Aaltjesmanagement in de akkerbouw
    Beers, T.G. van - \ 2010
    PPO AGV
    veldgewassen - plantenparasitaire nematoden - vrijlevende nematoden - nematodenbestrijding - nederland - identificatie - akkerbouw - field crops - plant parasitic nematodes - free living nematodes - nematode control - netherlands - identification - arable farming
    Deze brochure bevat de meest recente kennis en informatie over aaltjesherkenning en maatregelen voor aaltjesbeheersing. Leeswijzer Het herkennen van aaltjes is het begin van aaltjesbeheersing. In hoofdstuk 2 worden daarom de belangrijkste aaltjes in de akkerbouw beschreven en in beeld gebracht. Vervolgens worden in hoofdstuk 3 de stappen om een aaltjesprobleem aan te pakken schematisch weergegeven. De beheersing van het aaltjesprobleemen staat beschreven in hoofdstuk 4. Voorkomen van aaltjes op uw bedrijf is nog beter. Hoe u dat kunt realiseren staat beschreven in hoofdstuk 5. Hoofdstuk 6 gaat dieper in op de achtergronden van de diverse maatregelen. Hoofdstuk 7 gaat over de schade die aaltjes kunnen geven en welke factoren daarbij een rol spelen.
    Oormerken zonder problemen
    Schuiling, H.J. - \ 2010
    Lelystad : ASG veehouderij (Rapport / Animal Sciences Group 350) - 8
    schapen - geiten - identificatie - oormerken - dierenwelzijn - diergezondheid - sheep - goats - identification - ear tags - animal welfare - animal health
    Based on a research recommendations are given for an optimal method in applying ear tags in sheep and goat.
    Innovaties in de Boomkwekerij
    Baltissen, Ton - \ 2010
    forest nurseries - nurseries - innovations - cropping systems - mechanization - identification - monitors - sensors - rfid
    Heteroptera
    Dekkers, Dorine - \ 2009
    heteroptera - insects - hemiptera - determination - identification - zoogeography - keys - netherlands
    Fusarium in wintertarwe (2007 en 2008). Inventarisatie, identificatie en kwantificering van nieuwe soorten
    Waalwijk, C. ; Köhl, J. ; Vries, P.M. de; Lee, T. van der - \ 2009
    Wageningen : Plant Research International (Rapport / Plant Research International 272)
    triticum aestivum - tarwe - schimmelziekten - fusarium - identificatie - mycotoxinen - eu regelingen - gezondheid - diergezondheid - nederland - duitsland - frankrijk - triticum aestivum - wheat - fungal diseases - fusarium - identification - mycotoxins - eu regulations - health - animal health - netherlands - germany - france
    Fusarium-aarziekte of kalfjesrood is vanwege de opbrengstderving een probleem in granen. Feitelijk wordt Fusarium-aarziekte veroorzaakt door een complex van schimmels dat in steeds andere samenstelling het gewas belaagt. Van recenter datum is de zorg over het vermogen van verschillende Fusariumsoorten om mycotoxinen te produceren. Deze secundaire metabolieten vormen reeds in geringe hoeveelheden een bedreiging voor de gezondheid van mens en dier. De Europese Commissie heeft daarom actielimieten vastgesteld voor een aantal mycotoxinen, terwij; voor enkele andere deze regels aanstaande zijn (Verordening (EG) nr. 1881/2006; Verordening (EG) nr. 1126/2007). Vanwege de steeds strengere normen voor diverse mycotoxinen in voedsel en voer zijn bji ongunstige teeltcondities partijen niet vermarktbaar en kan een tekort aan het te verwerken graanproduct ontstaan
    RFID in de verse groente keten, nu en morgen (temperatuur- en vochtmonitoring)
    Bartels, Paul - \ 2009
    food chains - identification - radio waves - nutrition labeling - tracer techniques - vegetables - fresh products - rfid - logistics
    Plantenziektes bestrijden met genetische vingerafdruk
    Bonants, P.J.M. - \ 2009
    Kennis Online 6 (2009)okt. - p. 4 - 5.
    plantenziektebestrijding - plantenziekteverwekkers - polymerase-kettingreactie - identificatie - quarantaine organismen - fytosanitair beleid - moleculaire plantenziektekunde - moleculaire herkenning - plant disease control - plant pathogens - polymerase chain reaction - identification - quarantine organisms - phytosanitary policies - molecular plant pathology - molecular recognition
    Nederland speelt een belangrijke rol in een Europees project dat quarantaineorganismen wil voorzien van een DNA-streepjescode. Wageningen UR, de Plantenziektenkundige Dienst, en het Centraalbureau voor Schimmelcultures van de KNAW gaan samen met zeventien andere Europese onderzoeksinstituten op zoek naar de unieke streepjescode voor elke plantenplaag
    Report of species diagnosis of a tuna at Queens Products B.V. on 23 December 2009
    Couperus, A.S. - \ 2009
    IJmuiden : IMARES (Report / IMARES Wageningen UR C147/09) - 12
    voedselindustrie - etiketteren van voedingsmiddelen - productinformatie - visproducten - thunnus - morfologie - analyse - identificatie - food industry - nutrition labeling - merchandise information - fish products - thunnus - morphology - analysis - identification
    According to a company in the same marketsegment as Queen Products B.V. part of the tuna filet sold by Queens Products B.V. does not consist of the species that is mentioned on the label. According to DNA analysis filets were not from the species on the label, Albacore (Thunnus alalunga), but from Yellowfin tuna (T. albacares). The present intention of Queens Products is to check by means of DNA analysis of different lots of filets the originating species. A Spanish expert on DNA analysis who has travelled to the Netherlands to collect samples, has requested species identification by an independent scientist on the basis of morphological features as back up of the findings by means of DNA analysis
    Checklist of the Oribatid Mites of the Netherlands (Acari: Oribatida)
    Siepel, H. ; Zaitsev, A. ; Berg, M. - \ 2009
    Nederlandse Faunistische Mededelingen 30 (2009). - ISSN 0169-2453 - p. 83 - 112.
    oribatida - mijten - identificatie - soorten - oribatida - mites - identification - species
    More than fifty years ago Van der Hammen published the last checklist of oribatid mites (or moss mites) for the Netherlands. Since then the species number has almost doubled to 318 species, of which 100 are presented here for the first time. Brief data on occurence and nomenclature are provided for each species. A short list of fossil species known from the Netherlands is presented seperately
    Classificatie van planten - nieuwe inzichten en gevolgen voor de praktijk
    Hoffman, M.H.A. - \ 2009
    Dendroflora 2008 (2009)45. - ISSN 0374-7247 - p. 4 - 18.
    classificatie van rassen - planten - soorten - rassen (taxonomisch) - identificatie - variety classification - plants - species - races - identification
    Er zijn ongeveer 300.000 verschillende (hogere) plantensoorten, die onderling veel of weinig op elkaar lijken. Vroeger werden alle plantensoorten afzonderlijk benaamd, en was niet duidelijk hoe deze soorten verwant waren. Tegenwoordig worden soorten conform het systeem van Linnaeus ingedeeld in geslachten. Soorten die sterk verwant zijn aan elkaar hebben dezelfde geslachtsnaam. Geslachten worden op hun beurt weer ingedeeld in families en die op hun beurt weer in ordes, enzovoort. Op deze manier kent het plantenrijk een hiërarchisch indelingsysteem, met verwantschap als basis. Sterke verwantschap is meestal ook zichtbaar aan de uiterlijke gelijkenis. Soorten die veel op elkaar lijken en verwant zijn zitten in dezelfde groep. Verre verwanten zitten ver uit elkaar in het systeem. Om een plant goed te kunnen benamen, moet dus eerst uitgezocht worden aan welke andere soorten deze verwant is.
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