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.

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    The genus Romboutsia : genomic and functional characterization of novel bacteria dedicated to life in the intestinal tract
    Gerritsen, J. - \ 2015
    Wageningen University. Promotor(en): Hauke Smidt; Willem de Vos, co-promotor(en): G.T. Rijkers. - Wageningen : Wageningen University - ISBN 9789462572423 - 280
    darmmicro-organismen - voeding en gezondheid - microbiota van het spijsverteringskanaal - darmziekten - moleculaire technieken - probiotica - intestinal microorganisms - nutrition and health - gastrointestinal microbiota - intestinal diseases - molecular techniques - probiotics
    The genus Romboutsia: genomic and functional characterization of novel bacteria dedicated to life in the intestinal tract

    PhD thesis Jacoline Gerritsen, 2015


    Humans, like other mammals, are not single-species organisms, but they constitute in fact very complex ecosystems. The extensive network of host-microbe and microbe-microbe interactions is tremendously important for our health, and we are just starting to unravel the mechanisms by which microbes contribute to host health and disease.

    Especially the intestinal tract of both humans and mammals contains an enormous diversity of microbial species of which many still remain to be cultured and characterized. There are numerous diseases for which aberrations in composition and diversity of the intestinal microbiota have been reported. Probiotic microorganism defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” have the potential to modulate the intestinal microbiota and thereby contribute to health and well-being. To this end, the relative abundance of a specific bacterial phylotype, named CRIB, was found to be associated with probiotic-induced changes in gut microbiota and decreased severity of pancreatitis and associated sepsis in an experimental rat model for acute pancreatitis studies. Later, a representative of this phylotype (strain CRIB) was isolated, and characterized using a polyphasic taxonomic approach. The taxonomy of several closely related members of the family Peptostreptococcaceae was revised in order to provide a valid systematic name to the isolate, for which Romboutsia ilealis was chosen. It was found that the majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, however, the specific roles that Romboutsia species play in the intestinal tract are largely unknown. To gain more insight in metabolic and functional capabilities of members of the genus Romboutsia, efforts towards the isolation of additional representatives were undertaken. This ultimately led to the isolation of a human small intestine-derived representative (strain FRIFI) of another novel Romboutsia species which was given the name R. hominis. Characterization of both novel species of intestinal origin, i.e. R. ilealis and R. hominis, belonging to the genus Romboutsia at the genomic and functional level provided first insights into the genetic diversity within the genus Romboutsia and their adaptation to a life in the (upper) intestinal tract. To this end, Romboutsia species are flexible anaerobes that are adapted to a nutrient-rich environment in which carbohydrates and exogenous sources of amino acids and vitamins are abundantly available.

    Microbiomic approaches such as those employed in this study can be used to pinpoint specific commensal microbes that might have a beneficial effect on the health of the host. In addition, the combination of genomic and functional analyses with single organisms and complex communities can be used to identify microbial functionalities that are related to health and disease, which in turn can be used to select potential probiotic strains based on specific functional properties. Ultimately, these approaches will lead to the characterization of (new) beneficial commensal microbes that exert health-promoting effects, with the ultimate possibility for them to be exploited as next-generation probiotics.

    The use of molecular chemistry (pyrolysis-GC/MS) in the environmental interpretation of peat
    Schellekens, J. - \ 2013
    Wageningen University. Promotor(en): Thomas Kuijper, co-promotor(en): Peter Buurman. - Wageningen : Wageningen UR - ISBN 9789461737823 - 161
    turf - veengronden - vegetatie - degradatie - sphagnum - gewasanalyse - vegetatietypen - pyrolyse - moleculaire technieken - chemie - veenmoerassen - peat - peat soils - vegetation - degradation - sphagnum - plant analysis - vegetation types - pyrolysis - molecular techniques - chemistry - bogs


    The molecular composition of organic matter in peatlands reflects local conditions and stores information about botanical composition (plant source) as well as the degree of and conditions during decomposition. A reliable hydrological (and hence palaeoclimatological) interpretation of source and decomposition proxies in peatlands requires the understanding of the interactions between decomposition and botanical composition and the reaction of both to changes in the water table. Only few studies combined vegetation and decomposition characteristics to investigate peat OM dynamics and reconstruct environmental changes, and these included only a limited number of samples. In order to study the three-way relationship between botanical composition, decomposition and environmental conditions, pyrolysis-GC/MS of high-resolution sampled peat cores was used on two contrasting ombrotrophic peatlands. The two sites comprise a Sphagnum-dominated peatland in Tierra del Fuego (Argentina) and a graminoid-dominated peatland in Galicia (Spain). The purpose of this study was to examine the use of analytical pyrolysis in the environmental interpretation of peat profiles and to gain an improved understanding of peat OM dynamics and thereby develop parameters that reliably reflect past environmental conditions.

    The molecular composition of the Sphagnum-dominated Harberton peatland was first explored for a selection of samples. Several peat fractions have been analysed, including NaOH-extract, NaOH-insoluble residue and bulk sample. A large number of pyrolysis products was identified and quantified for all peat samples; additionally total C, N and ash content were measured. Molecular parameters were identified by a systematic methodological approach. Peatland plants have been analysed in search for specific markers. Factor analysis was used to reduce the number of pyrolysis products for quantification and to assess differences in peat chemistry and relate these to environmental factors. This resulted in a number of molecular parameters that reflect botanical changes, (an)aerobic decomposition and fire incidence.

    The results of the different peat fractions and plant analysis were applied to a large number of bulk samples (67), and used to reconstruct the 12,000 years of vegetation history of the Harberton core, which was then interpreted in terms of past hydrological conditions. The C:N ratio showed a perfect agreement with the botanical composition according to pyrolytic plant markers. It appeared that the n-alkane distribution showed remarkable changes with respect to shifts in the abundance of Sphagnum. Consequently, the detailed vegetation reconstruction was used to discuss the application of the n-alkane distribution in ombrotrophic peat. The simultaneous effects of botanical shifts (source material) and decomposition may cause conflicting hydrological interpretations for non-specific plant markers such as n-alkanes. The results indicated a considerable effect of aerobic decomposition on the distribution of n-alkanes. Although pyrolysis is not the regular method to establish the n-alkane distribution, comparison of n-alkanes in the NaOH-extract and residue peat samples supported the findings. The results emphasise the importance of combining vegetation and decomposition characteristics.

    For the graminoid-dominated Penido Vello peatland, all 101 bulk peat samples of the 3 m thick peat deposit have been analysed. In addition to the search for specific compounds of peatland plants, the same pyrolysis products were quantified for plant pyrolysates and peat. Depth records of plant markers agreed well with their preferential habitat, with the degree of decomposition and with the transition from minerotrophic to ombrotrophic peat. Factor analysis was used to reconstruct past hydrology. The results showed the importance of high-resolution sampling through the higher correlations between molecular parameters in the part sampled each 2 cm compared to 5 cm. Furthermore, good correlations of pyrolysis results were found with mineral content, solid-state 13C CPMAS NMR data and total N.

    The hydrological reconstruction based on depth records of plant markers and factor scores obtained by factor analysis of all quantified pyrolysis products, and the low contribution of Sphagnumto the graminoid-dominated Penido Vello peat allowed studying the effects of source and decay on the lignin composition. A large number of lignin pyrolysis products were quantified for peatland plants and for the three different peat fractions for a selection of 15 samples. Lignin composition of woody and graminoid plant species were compared as well as the lignin composition in different peat fractions, and their relation to source or decay was established.

    To determine whether the lignin parameters, derived from analysis of plants and peat fractions, can be used to reconstruct peat environment, they were applied to all 51 bulk peat samples of the upper meter of the Penido Vello core. The results show a strong effect of vegetation type and anaerobicity on generally-used lignin decomposition proxies, which indicates that such proxies are not reliable without information on the context.

    To examine the interaction between vegetation type and decomposition processes, the results of Sphagnum-dominated peat and graminoid-dominated peat were combined. In addition to the well-known pyrolytic marker from Sphagnum (4-isopropenylphenol), depth records of pyrolysis products specific for lichens and graminoids functioned well in both peatlands and are considered reliable markers for application in other peatlands. A number of other identified markers only functioned well within one of both peatlands. The different functioning of these markers in the two peatlands emphasises the importance of plant analysis prior to the use of pyrolytic biomarkers with low specificity, but also shows that supposedly non-specific pyrolysis products can be specific within a certain peatland ecosystem. The use of different peat fractions (NaOH-extractable and non-extractable peat) provided information on the degree of decomposition and allowed comparison with studies on peat humic acids and humin, and the generally applied colorimetric method to determine peat humification. Furthermore, the comparison of pyrolysates of extracts and residues for a selection of peat samples, in combination with factor analysis, allowed separation of the effects of source, and several stages of aerobic and anaerobic decay. Degradation of lignin-cellulose (vascular plants) and polyphenol-cellulose (Sphagnum) is discussed using the abundance of their markers (lignin moieties, levoglucosan and 4-isopropenylphenol) in pyrolysates of the different peat fractions, and gives insight into degradation mechanisms. The results indicated that, in Sphagnum litter, polyphenols are more easily degraded than polysaccharides. Comparison of pyrolysis results and C:N ratio showed that differences in litter quality between Sphagnum and vascular plants is a major factor that determines the variance of C:N with depth. Large part of the variation in C:N in Sphagnum-dominated peat is caused by decomposition rather than small increases of vascular plants upon drier conditions, while in graminoid-dominated peat this is not true and several processes may disturb the effect of mass loss on the C:N ratio. The C:N ratio can thus be a consistent decomposition proxy in Sphagnum-dominated peat but not in graminoid-dominated peat. Pyrolysis-GC/MS in combination with the applied research design provided detailed chemical information that gave insight in both vegetation and decomposition characteristics. This methodology thus has a high potential for the reconstruction of past environmental conditions.

    'Intraspecific pathogen variation' Verslag KNPV/Plantum/EPS-eendagsconferentie : Wageningen, 22 januari 2013
    Folkertsma, R.T. ; Goverse, A. ; Posthuma, E. ; Gilijamse, T. - \ 2013
    Gewasbescherming 44 (2013)2. - ISSN 0166-6495 - p. 32 - 34.
    plantenziekteverwekkers - genetische variatie - genotypische variatie - dna-sequencing - moleculaire technieken - moleculaire genetica - plantenziekten - conferenties - plant pathogens - genetic variation - genetic variance - dna sequencing - molecular techniques - molecular genetics - plant diseases - conferences
    Dinsdag 22 januari 2013 werd in Wageningen een eendagsconferentie gehouden getiteld ‘Intraspecific pathogen variation - implications and opportunities’. Deze conferentie werd georganiseerd naar aanleiding van discussies over het werken met intraspecifieke variatie voor diagnostiek en veredeling binnen de Nematodenwerkgroep van de KNPV en de Isolaten-beheerwerkgroep van Plantum. Het doel van de bijeenkomst was a.) onderzoekers uit de private en de publieke sector samenbrengen om recente ontwikkelingen te bespreken in fundamentele en toegepaste aspecten van het werken met intraspecifieke variatie, en b.) het stimuleren van uitwisselen van ideeën binnen en tussen beide groepen, voor mogelijke vervolginitiatieven.
    Genomics in de fokkerij: in tien jaar van topwetenschap naar big business
    Arendonk, J.A.M. van; Groenen, M. - \ 2013
    Kennis Online 10 (2013)mei. - p. 7 - 8.
    dierveredeling - genomica - fokkerijmethoden - moleculaire technieken - single nucleotide polymorphism - selectiemethoden - melkvee - varkens - genomen - animal breeding - genomics - animal breeding methods - molecular techniques - single nucleotide polymorphism - selection methods - dairy cattle - pigs - genomes
    Genomics was tien jaar geleden topwetenschap die alleen bedreven werd in dure laboratoria van universiteiten en onderzoeksinstituten. Nu gebruiken fokbedrijven DNA-chips om al op jonge leeftijd te kunnen voorspellen welke stier het beste sperma levert, en om te zien of berengeur bij varkens door een slim fokprogramma kan worden voorkomen.
    Genetic control and variation in turkey: molecular insights in selection
    Aslam, M.L. - \ 2012
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): John Bastiaansen; Richard Crooijmans. - S.l. : s.n. - ISBN 9789461733092 - 184
    meleagris - kalkoenen - genetische variatie - moleculaire veredeling - selectie - genetische kartering - loci voor kwantitatief kenmerk - moleculaire technieken - dierveredeling - meleagris - turkeys - genetic variation - molecular breeding - selection - genetic mapping - quantitative trait loci - molecular techniques - animal breeding

    The turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat type bird as egg production of this species is very low. Turkey is the second largest contributor to the world’s poultry meat production after chicken. Understanding the etiology and biology underlying production and health traits is very important for the genetic improvement of these traits in the desired direction and to avoid undesired side-effects. The aim of the research described in this thesis was to interrogate the genetics of turkey traits related to meat production and to investigate the genetic diversity of commercial and heritage turkey populations.
    Different analyses were performed that included the estimation of genetic and (common) environmental variances for growth (body weight as well as growth curve traits), breast meat yield and meat quality traits in turkeys. I describe the construction of a single nucleotide polymorphism (SNP) based linkage map of turkey and its comparison with the physical map of chicken to investigate genome structural differences between these highly important poultry production species. Two inter-, and 57 intra-chromosomal rearrangements between these two species were confirmed or discovered which is a low number in comparison to mammals and lead to the conclusion that turkey and chicken have highly conserved genomic structure. I used the linkage map of turkey together with individual phenotypes to map quantitative trait loci (QTL) in the same population for the traits described above. Results showed quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on the 21 chromosomes. The next step, after the analyses on the reference population was to investigate the genomic variation in turkeys Next generation sequencing was used to investigate genome variation and the discovery of genome-wide signatures of selection in the turkey respectively. Sequencing was performed on 32 individuals from eleven different turkey populations (seven commercial, three heritage and a South Mexican wild population). Analysis of next generation sequencing data resulted in the detection of 5.49 million putative SNPs compared to the reference genome. The average frequency of heterozygous nucleotide positions in individual turkeys was 1.07 Kb-1 which is substantially lower than in chicken and pigs. The SNPs were subsequently used for the analysis of genetic diversity between the different populations. Genetic diversity analysis using pairwise Nei’s genetic distance among all the individuals from the 11 turkey populations showed that all of the commercial lines branched from a single node relative to the heritage varieties and the ancestral turkey population, indicating that commercial lines appear to share a common origin.
    After assessing genome wide variation and diversity between breeds, the SNP data from ten of the turkey populations (29 individuals) was used to detect selective sweep regions. Across the turkey populations, 54 genomic regions with significant evidence for a selective sweep were detected. These sweeps were distributed over 14 different chromosomes. This study has investigated the genetics i.e. analysis of variances and QTL mapping related to economically important traits in turkey production and the genomic variation of turkey. Furthermore, this study has also created resources e.g. millions of discovered SNPs for subsequent genomic work in the turkey such as to discover variant (s) for both minor and major effects on traits of economic importance, and a high-resolution linkage map can be developed.

    Verbetering bloeizekerheid bij potplanten en snijbloemen met behulp van moleculaire toetsen
    Kromwijk, J.A.M. ; Noort, F.R. van; Verhoef, N. ; Balk, P. ; Lamers, R. - \ 2012
    Bleiswijk : Wageningen UR Glastuinbouw (Rapporten GTB 1168) - 44
    potplanten - snijbloemen - sierteelt - glastuinbouw - bloei - verbetering - moleculaire technieken - tests - nederland - pot plants - cut flowers - ornamental horticulture - greenhouse horticulture - flowering - improvement - molecular techniques - tests - netherlands
    Abstract In several ornamentals there is insufficient certainty about the flowering results. Wageningen UR Greenhouse Horticulture and NSure have investigated whether flowering results can be improved with the development of molecular tests. In crops such as snowball (Viburnum opulus 'Roseum’), Hydrangea, azalea and Syringa flower buds go into winter dormancy in autumn. Flowering results of these crops can be improved when it is possible to measure when winter dormancy is sufficiently broken to force these crops successfully. For Viburnum a molecular test has been developed and successfully tested. For Hippeastrum, Bromelia, Cymbidium, Miltonia, Nerine and Zantedeschia it was investigated whether development of a molecular test can improve flowering results. For Cymbidium a greenhouse experiment was conducted with 0, 2, 4, 8, 13 and 16 weeks 13 oC from week 44 - 2010 and plant samples were collected at the end of the treatments. As plants stood longer at 13 oC, the number of inflorescences autumn 2011 increased. The collected samples can be used to develop a molecular test in the future.
    Detectie en beheersing van bacterierot veroorzaakt door Pseudomonas cattleyae in Phalaenopsis
    Ludeking, D.J.W. ; Hamelink, R. ; Kromwijk, J.A.M. ; Schenk, M.F. ; Vermunt, A. ; Woets, F. - \ 2011
    Bleiswijk : Wageningen UR Glastuinbouw (Rapporten GTB 1096) - 31
    phalaenopsis - bacterieziekten - infectie - pseudomonas - bladvlekkenziekte - black spot - moleculaire technieken - relatieve vochtigheid - waterzuivering - invloeden - phalaenopsis - bacterial diseases - infection - pseudomonas - leaf spotting - black spot - molecular techniques - relative humidity - water treatment - influences
    Phalaenopsis growers suffer from mayor losses up to 20% due to bacterial spot. This bacterial infection in caused by the Acidovorax avenae subsp. cattleyae. In practice this bacterial disease is also known as Pseudomonas. This bacterium is causing black leaf spots with a yellow border. Pseudomonas cattleyae is very contagious and is promoted by high temperatures en moist conditions. In this project Groen Agro Control laboratory (Delfgauw) has developed a molecular analysis method to detect Pseudomonas cattleyae in different matrices. The influence of the relative humidity on the development of Pseudomonas cattleyae is investigated during this research. The results show that a relative humidity of 90% strongly promotes infection of the bacteria. A relative humidity of 75% shows no extra dispersion of Pseudomonas cattleyae compared to a greenhouse compartment with a continuous relative humidity of 60%. This knowledge offers the opportunity to safe energy in the cultivation of Phalaenopsis. During this research the effects of water treatments on the dispersion of Pseudomonas cattleyae have been investigated. The results show that a treatment with hydrogen peroxide (20 ppm) offers the best reduction of dispersion. This treatment turns out to be better than the control and all other treatments. This research has led to new insights about the dispersal and optimal growing conditions of this bacteria, but leads to new questions. Questions, about other different dosages and the effects of other water treatments, but also about the optimal level to promote plant growth and reduce bacterial infections, have to be investigated in new research.
    Levend of dood, dat is de vraag!
    Lee, T.A.J. van der; Leeuwen, G. van; Haan, E. de; Helder, J. ; Koenraadt, H. ; Bonants, P.J.M. - \ 2011
    Gewasbescherming 42 (2011)2. - ISSN 0166-6495 - p. 71 - 75.
    moleculaire plantenziektekunde - plantenziekten - plantenplagen - moleculaire detectie - quarantaine organismen - infectiviteit - moleculaire technieken - molecular plant pathology - plant diseases - plant pests - molecular detection - quarantine organisms - infectivity - molecular techniques
    In de literatuur zijn voor de detectie van plantenpathogenen diverse methodieken beschreven. De biologische methodieken detecteren alleen levende organismen. Morfologische, serologische en moleculaire technieken maken mmestal geen onderscheid tussen dood en levend of infectieus en niet infectieus. Met name voor quarantaineorganismen is het onderscheid tussen levende en dode pathogenen van essentieel belang. Binnen het FES-programma 'Versterking infrastructuur plantgezondheid' is binnen werkpakket 3 'Ontwikkeling van methoden voor het aantonen van vitaliteit van plantenpathogenen' gewerkt aan de detectie van vitaliteit in nematoden, schimmels en bacteriën.
    CSI ook in de Plantenwereld
    Bonants, P.J.M. ; Lee, T.A.J. van der - \ 2011
    Gewasbescherming 42 (2011)2. - ISSN 0166-6495 - p. 66 - 71.
    plantenplagen - plantenziekten - moleculaire detectie - polymerase-kettingreactie - quarantaine organismen - moleculaire plantenziektekunde - moleculaire herkenning - moleculaire technieken - plant pests - plant diseases - molecular detection - polymerase chain reaction - quarantine organisms - molecular plant pathology - molecular recognition - molecular techniques
    In de land- en tuinbouw heeft de ontwikkeling van (moleculaire) detectiemethoden van plantenpathogenen de laatste jaren een hoge vlucht genomen. Inmiddels worden deze methoden al grootschalig toegepast in de praktijk. Werd in het begin alleen conventionele polymerase chain reaction (PCR) ingezet voor moleculaire detectie, momenteel vindt ook real-time PCR meer en meer ingang. Binnen het FES-programma ‘Versterking infrastructuur plantgezondheid’ zijn binnen het werkpakket ‘Identificatie- en Detectiemethoden’ vele projecten uitgevoerd om de ‘daders’ van aantastingen te kunnen identificeren. De focus was hierbij gericht op quarantaineorganismen.
    Innovatieve merkertechnieken t.b.v. resistentieveredeling bij lelie
    Tuyl, J.M. van - \ 2008
    Wageningen : Plant Research International - 32
    lilium - lelies - resistentieveredeling - moleculaire technieken - plantenziektebestrijding - bloembollen - lilium - lilies - resistance breeding - molecular techniques - plant disease control - ornamental bulbs
    De nieuwste moleculaire merker technieken (GISH en FISH chromosoomkleurings-technieken; NBS-profyling en DArT moleculaire merkertechnieken) zijn toegepast op lelie met als doel de overdracht van chromosoomfragmenten in kruisingen tussen verschillende leliehybriden (LA OA) te volgen, en in een vroeg stadium te selecteren op resistentie tegen Fusarium, Botrytis en virus. Hierdoor krijgt men inzicht in de vererving van resistenties in deze hybride-kruisingen, en kan men gerichter en efficiënter veredelen.
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