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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Differences in transcriptional responses to acute and chronic dietary interventions with fatty acids
Matualatupauw, Juri C. - \ 2017
Wageningen University. Promotor(en): Sander Kersten, co-promotor(en): Lydia Afman; J. Bouwman. - Wageningen : Wageningen University - ISBN 9789463432078 - 172
fatty acids - gene expression - genotyping - phenotypes - nutritional intervention - transcriptomics - fish oils - apolipoprotein e - adipose tissue - microarrays - polymerase chain reaction - vetzuren - genexpressie - fenotypen - maatregel op voedingsgebied - transcriptomica - visoliën - apolipoproteïne e - vetweefsel - polymerase-kettingreactie

Various types of dietary fatty acids have different effects on human health. The aim of this thesis was to increase our understanding of the molecular mechanisms underlying the effects of dietary fatty acids. To do this, we examined changes in whole genome gene expression profiles upon both acute as well as longer term dietary fatty acid interventions. Furthermore, from previous research, it is clear that large inter-individual differences in the response to dietary fatty acids exist. We used whole genome gene expression analyses to increase our understanding of the mechanisms underlying some of these inter-individual differences.

Many modifiable and non-modifiable factors can be the cause of these inter-individual differences. In chapter 2, we reviewed all studies that examined differences in the transcriptional response to dietary interventions based on the presence of one of these factors. These include gender, age, BMI, body composition, blood lipid levels and gut microbial composition. We conclude that transcriptome analyses are well-suited for studying the underlying mechanisms behind these differences in the response to diet. Nevertheless, the number of studies that use this approach remains limited.

Another factor that may modify the response to a dietary intervention is genetics, e.g. the apolipoprotein E4 (APOE4) variant. People who carry the APOE4 allele have an increased risk of cardiovascular disease. Fish-oil supplementation may help in the prevention of cardiovascular disease, though inter-individual differences in the response to n-3 polyunsaturated fatty acids on gene expression profiles have been observed. In chapter 3, we aimed to assess the impact of APOE4 on peripheral blood mononuclear cell (PBMC) whole genome gene expression at baseline and following a 6-month fish-oil intervention. We observed increased gene expression of IFN signaling and cholesterol biosynthesis pathways in APOE4 carriers, which might explain part of the association between APOE4 and CVD. Furthermore, fish-oil supplementation may be beneficial by decreasing interferon signalling-related gene expression in APOE4 carriers.

Another long-term dietary intervention with fatty acids was studied in chapter 4. We examined the effect of a 12-week high medium-chain saturated fatty acid diet on subcutaneous adipose tissue gene expression profiles. We observed increased expression of genes involved in oxidative energy metabolism and decreased inflammation-related gene expression due to the high medium-chain saturated fatty acid intake. Considering the role of the adipose tissue in sustaining the low-grade inflammation that is associated with obesity, these findings may be indicative of a more anti-inflammatory phenotype of the adipose tissue. We concluded that medium-chain saturated fatty acids may potentially have beneficial effects on adipose tissue functioning.

Besides studying the effects of long-term interventions with fatty acids on whole genome gene expression, we also examined the effects of acute high-fat challenges. In chapter 5, we determined the additional value of determining whole genome gene expression changes in response to a high-fat challenge compared to assessment at fasting only. In addition, we aimed to identify whether a 4 week high-fat high-calorie diet can induce a shift in gene expression profiles in healthy subjects towards a metabolic syndrome-like gene expression profile. We found that fasting whole blood whole genome gene expression profiles are highly responsive to a 4-week high-fat high-calorie diet, with changes in in the direction of a metabolic syndrome-like gene expression profile. High-fat challenge responses in healthy subjects show only minimal changes in gene expression upon the dietary intervention and a marginal shift in the direction of the metabolic syndrome. We concluded that fasting gene expression profiles are more responsive compared to high-fat challenge responses to a 4-week high-fat high-calorie diet.

Besides chapter 5, several other studies have also examined changes in whole genome gene expression in blood cells induced by high-fat challenges. In chapter 6, we combined microarray data from four high-fat challenge studies varying in study population, challenge composition and research laboratory. By performing this meta-analysis, we showed a general PBMC whole genome gene expression response to a high-fat challenge. We concluded that a meta-analysis provides added value for the discovery of consistently differentially expressed genes and pathways compared to selecting only those genes and pathways that are identified in all separate studies.

In conclusion, in this thesis we showed differences in the whole genome gene expression response to fish-oil supplementation in PBMCs of APOE4 carriers vs non-carriers. Furthermore, the effects on whole genome gene expression of the two long-term dietary interventions, i.e. the fish-oil supplementation in PBMCs of APOE4 carriers and the high medium-chain saturated fatty acid diet in adipose tissue, may be beneficial by downregulation of gene expression related to inflammation. We also showed that whole genome gene expression responses to high-fat challenges are affected by a 4-week high-fat high-calorie diet, though changes in fasting gene expression profiles are much more pronounced. Finally, we showed the value of meta-analysis of microarray data in high-fat challenge studies for identifying the general response to a high-fat challenge.

Anaerobic microbial processes for energy conservation and biotransformation of pollutants
Luz Ferreira Martins Paulo, Lara da - \ 2017
Wageningen University. Promotor(en): Fons Stams, co-promotor(en): Diana Machado de Sousa. - Wageningen : Wageningen University - ISBN 9789463431125 - 234
anaerobic microbiology - anaerobes - energy conservation - biotransformation - pollutants - heavy metals - sulfates (inorganic salts) - nickel - cobalt - methanosarcina barkeri - genomics - polymerase chain reaction - anaërobe microbiologie - anaërobe micro-organismen - energiebehoud - biotransformatie - verontreinigende stoffen - zware metalen - sulfaten (anorganische zouten) - nikkel - kobalt - genomica - polymerase-kettingreactie

Anaerobic microbial processes are commonly applied in the treatment of domestic and industrial wastewaters. Anaerobic digestion (AD) of wastewater has received a great deal of attention, but many aspects related to the complex interactions between microorganism, and how that is affected by the presence of certain toxic, are not yet fully understood. A particular case of this is the effect of heavy metals or chlorinated compounds. These compounds are known to have a strong impact in methanogens, a phylogenetic diverse group responsible for the last step of the AD process. The negative effect of sulphate towards methanogenesis is mainly related to outcompetition of methanogens by sulphate-reducing bacteria (SRB), or to toxicity caused by the sulphide generated from sulphate reduction. Heavy metals are part of many enzymes and cofactors and, in low concentrations, may beneficiate microbial activity. However, high concentrations of metals may disrupt enzyme function and structure. In cases where metal concentration is high, the presence of sulphate or sulphide might be favourable because sulphide precipitate with metals and detoxify the environment. In Chapter 2 we provide a review on the current knowledge on the effects of heavy metals and sulphate on AD, with special focus on methanogenesis. From this literature study, it came out that the influence of some metals, such as Co, is not extensively studied and that the potential of biologically produced sulphide as metal detoxification method in AD is still quite unexplored. In Chapter 3 we explored different strategies to improve methane production. Low concentrations of Ni and Co were supplemented to anaerobic sludge and the impact on methane production was evaluated. Although in contrast with other studies, no beneficial effect of metal supplementation was observed. Further on, the impact of high concentrations of Ni and Co added to anaerobic sludge was evaluated, as well as the use of sulphide as a detoxification strategy. This was evaluated in terms of impact on methane production and in changes in the microbial communities. The results showed that sulphide can be used as a method for metal detoxification, but in the case of biological produced sulphide, the competition between SRB and methanogens needs to be considered.

Chlorinated compounds are widely used and commonly found in wastewaters. Several methanogenic metal-containing cofactors are reported to be involved in reductive dechlorination. Therefore, in Chapters 4 and 5 the potential of metal supplementation to enhance the dechlorination process was studied. In Chapter 4, the enrichment of methanogenic cultures able to perform reductive dechlorination of 1,2-dichloroethene (DCE) and tetrachlorethene (TCE) using different inoculum sources and substrates is described. Differences in physiological performance and in the microbial communities were evaluated. The results showed that the microbial community can be influenced by inoculum and substrate as well as by the chlorinated compound used. The enriched cultures presenting the best dechlorination performance were selected and used for metal supplementation studies with Ni, Co, and Fe. The results showed a clear positive impact of metal addition, both on methane production and reductive dechlorination. Further research on metal supplementation to enhance dechlorination was performed in pure cultures of Methanosarcina barkeri, a methanogen known to be able to reduce DCE (Chapter 5). In this case, it was observed that metal supplementation could improve methane production and reductive dechlorination, but the effect is dependent on the metal and concentration used. It was found that methanogenesis and reductive dechlorination can be affected in a different way by the same metal.

Finally, in Chapter 6 the impact of sulphate on a methane-producing bioelectrochemical system (BES), an emerging technology that can be applied to wastewater treatment, was studied. The results showed an unexpected fast sulphate removal in the system and a limited impact caused by sulphate addition on methane production. The sulphate removal could only partially be explained by microbial activity, but the results demonstrated the ability of microbial communities to evolve and adapt to new operational conditions.

In conclusion, the work presented in this thesis gave insights on the impact of heavy metals and sulphate in methanogenic systems. Furthermore, different approaches to maximise methane production were evaluated. In particular, it was shown that metal supplementation can be a promising strategy to improve anaerobic microbial processes, such as methanogenesis and reductive dechlorination.

Characterization of Coxiella burnetii outbreak strains
Kuley, Runa - \ 2017
Wageningen University. Promotor(en): Mari Smits; Jerry Wells, co-promotor(en): Alex Bossers. - Wageningen : Wageningen University - ISBN 9789463431514 - 226
coxiella burnetii - q fever - outbreaks - strains - characterization - pathogenesis - zoonoses - virulence - dna sequencing - polymerase chain reaction - livestock farming - netherlands - q-koorts - uitbraken (ziekten) - stammen (biologisch) - karakterisering - pathogenese - zoönosen - virulentie - dna-sequencing - polymerase-kettingreactie - veehouderij - nederland

Q fever is a worldwide zoonotic infectious disease caused by the bacterium Coxiella burnetii. During 2007-2010, the largest Q fever outbreak was reported in The Netherlands, where more than 4000 human cases were registered showing a serious burden of the disease. During this outbreak, goats harboring predominantly the CbNL01 genotype strain were identified as the major source of disease in humans and drastic measures such as mass culling of infected goats were implemented to reduce the spread of the pathogen and control the disease. In order to minimize such complications in the future, it is crucial to have a thorough understanding of the disease causing pathogen and to develop effective Q fever vaccines. The causes of the large Dutch outbreak are not well-understood and one of the main reasons speculated were the hyper-virulent behavior of the circulating C. burnetii isolates. The research described in this thesis focuses on the characterization of C. burnetii outbreak strains isolated from infected goats, cattle, sheep and human clinical materials. Our studies were initiated to better understand the bacterial pathogenesis, virulence, evolution, adaptations in various environments, host immune responses and to identify pathogen related factors that have modulated the disease outbreak. We specifically aimed to identify the virulence factors and mechanisms that contributed to the increased zoonotic potential of the strain associated with the Dutch Q fever outbreak.

The studies presented in this thesis majorly applied Pathogenomic approaches at the genome and transcriptome level to decipher host-pathogen interactions and to develop new tools to study C. burnetii infections. A transcriptome analysis of the outbreak C. burnetii strain of the CbNL01 genotype grown under in vivo and in vitro conditions resulted in the identification of distinct metabolic adaptations and virulence mechanisms of the bacterium. Detailed comparative analysis of complete genome sequences of C. burnetii strains showed a high similarity between strains of the same genotype. Genome sequences of the Dutch outbreak CbNL01 genotype strains were more divergent than the genome sequences of the less prevalent CbNL12 genotype strains and the NM reference strain. The analysis also showed that the high virulence of the outbreak strains was not associated with acquiring novel virulence-related genes arguing against the idea that the Dutch outbreak was due to emergence of hyper-virulent strains though horizontal gene transfer. Among the prominent genetic differences in the CbNL01 outbreak strains compared to CbNL12 and NM, were the presence of several point mutations and increased transposon mediated genome plasticity, which might have contributed to its epidemic potential. Point mutations, especially in a large number of membrane proteins, could also have contributed to the increased zoonotic potential of CbNL01 strains allowing this clone to escape the host immune responses in goats and humans. In addition, mutations in critical genes involved in virulence and evasion of the host immune system could be potentially involved in the increased virulence of the CbNL01 outbreak strains. On the contrary, studies on host immune responses in an in vivo (experimental infections in mice) and an in vitro (human PBMC’s stimulation) model did not show any difference associated with the strain genotype. However, differences in immune responses were found to be associated with the host-origin of the C. burnetii strains. Among different host-origin strains, strains derived from goats and humans generated significantly lower innate and adaptive immune responses than strains derived from cattle, whereas no differences in immune responses were observed when strains were grouped based upon their genotype. These observations support immune evasions as a major virulence strategy of goat and human strains in hosts and further suggest that bacteria originating from goats have a greater potential to cause outbreaks in humans. This indicates that for Q fever prevention purposes goats should be efficiently monitored for the presence of C. burnetii. Taken together, the results described in this thesis suggest that the virulence potential of C. burnetii strains is not only based on genetic differences, but also on other host-adaptation mechanisms such as transposition of genomic elements and/or differential regulation of gene expression. Finally, the results from this thesis provide a framework for future studies in the development of vaccines and diagnostic tools for Q fever.

Interplay between gut microbiota and antibiotics
Jesus Bello Gonzalez, Teresita de - \ 2016
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): M.W.J. van Passel. - Wageningen : Wageningen University - ISBN 9789463430043 - 293
antibiotics - intestinal microorganisms - aminoglycoside antibiotics - enterococcus - interactions - zoo animals - man - patients - dna sequencing - polymerase chain reaction - antibiotica - darmmicro-organismen - aminoglycoside antibiotica - interacties - dierentuindieren - mens - patiënten - dna-sequencing - polymerase-kettingreactie

The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria.

Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them.

The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence.

Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype. In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated.

Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosyl-hydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of non-human primates, the applicability of Human Intestinal Tract Chip (HITChip) to study the gut microbiota composition of these animals was assessed, including a comparison with healthy human volunteers (Chapter 3). It was concluded that the HITChip can be successfully applied to the gut microbiota of closely related hominids, and the microbiota dynamics can therefore be quickly assessed by the HITChip.

In Chapter 4, a combination of 16S rRNA phylogenetic profiling using the HITChip and metagenomics sequencing was implemented on samples from a single ICU hospitalized patient that received antibiotic prophylactic therapy (Selective Digestive Decontamination - SDD). The different approaches showed a highly dynamic microbiota composition over time and the prevalence of aminoglycoside resistance genes harbored by a member of the commensal anaerobic microbiota, highlighting the role of the commensal microbiota as a reservoir of antibiotic resistance genes. As an extension of this study (Chapter 5), 11 ICU patients receiving SDD were followed using 10 healthy individuals as a control group to compare the diversity and dynamics of the gut microbiota and resistome by HITChip and nanolitre-scale quantitative PCRs, respectively. The microbial diversity of the healthy individuals was higher compared to ICU patients, and it was less dynamic compared to ICU patients under antibiotic treatment. Likewise, the levels of antibiotic resistance genes increased in ICU patients compared to healthy individuals, indicating that during ICU hospitalization and the SDD, gut microbiota diversity and dynamics are profoundly affected, including the selection of antibiotic resistance in anaerobic commensal bacteria.

This was further expanded in an extensive study focusing on colonization dynamics with antibiotic resistant bacteria as described in Chapter 6. This was performed in the same group of ICU-hospitalized patients receiving SDD therapy and showed that by using a range of culture media and selective conditions a variety of taxonomic groups could be isolated, including aerobic and anaerobic antibiotic resistant bacteria. The overall composition of the faecal microbiota detected by HITChip indicated mainly a decrease of Enterobacteriaceae and an increase of the enterococcal population. Since critically ill patients are susceptible to hospital-acquired infections and the control of the emergence of antibiotic resistance is crucial to improve therapeutic outcomes, an extended analysis of the Enterococcus colonization dynamics in this group of patients by cultivation and phenotypic and genotypic characterization of the isolates provided new information about carriage of antibiotic resistance and virulence factor encoding genes (Chapter 7). It also highlighted the opportunity for the exchange of resistance and virulence genes, which could increase the risk of acquiring nosocomial infections.

Next, chapter 8 described the implementation of high-throughput cultivation-based screening using the Microdish platform combined with high-throughput sequencing (MiSeq) using faecal samples from ICU patients receiving SDD. This allowed for the recovery of previously uncultivable bacteria, including a pure culture of a close relative of Sellimonas intestinalis BR72T that was isolated from media containing tobramycin, cefotaxime and polymyxin E. This strain could therefore represent a potential antibiotic resistance reservoir.

In conclusion, this thesis provides broad insight into the diversity and dynamics of the gut microbiota and resistome in ICU hospitalized patients receiving SDD therapy as well as the dynamics of colonization with antibiotic resistant bacteria. Especially our extensive study of the colonization dynamics of Enterococcus spp. during ICU stay reinforced the notion that SDD therapy does not cover this group of bacteria and highlights the importance of a critical control of the emergence of antibiotic resistance in enterococci and their spread and dissemination as known potential pathogens.

Furthermore, the extensive use of antibiotics could select for an increase in the rate of antibiotic resistance against aminoglycosides and beta-lactams, indicating that a control in the use of broad spectrum antibiotics needs to be considered. In addition, this thesis provides evidence regarding the possible genetic background involved in the subsistence phenotype, however, future studies on metabolic pathways could provide novel insight into the underlying mechanisms.

Breaking down barriers: construction of a hybrid heterochiral membrane
Siliakus, Melvin - \ 2016
Wageningen University. Promotor(en): John van der Oost, co-promotor(en): Servé Kengen. - Wageningen : Wageningen University - ISBN 9789462579293 - 237
membranes - engineering - escherichia coli - fatty acids - isoprenoids - archaea - thermococcus kodakarensis - polymerase chain reaction - gene knock-out - dna modification - membranen - vetzuren - isoprenoïden - polymerase-kettingreactie - inactivering van genen - dna-modificatie

Because of a chemical disparity between Archaeal and Bacterial membrane-lipids, these organisms thrive under distinct environmental conditions. Archaea are generally more resistant to extreme habitats like low pH, high temperature or presence of solvents. It has therefore long been hypothesized that the archaeal lipids provide archaeal cells with a higher robustness than bacterial lipids do for Bacteria. A recent study in which bacterial and archaeal lipids were mixed to form hybrid vesicles “lipid enclosed round structures”, for instance showed a higher temperature dependent stability than either the bacterial or archaeal lipid vesicles separately. In the present study, we therefore introduced the enzymatic machinery for assembly of archaeal lipids into the bacterium Escherichia coli. This engineering led to cells with a mixed membrane at a surprisingly high amount of 28% archaeal lipids. Although the intervention led to severe morphological malformations, the cells indeed showed an increased robustness to extreme cold and butanol.

IAG ring test animal proteins 2016
Raamsdonk, L.W.D. van; Rhee, N.E. van de; Scholtens-Toma, I.M.J. ; Prins, T.W. ; Vliege, J.J.M. ; Pinckaers, V.G.Z. - \ 2016
Wageningen : RIKILT Wageningen UR (RIKILT report 2016.008) - 31 p.
ring test - animal proteins - analytical methods - microscopy - fish feeding - animal health - polymerase chain reaction - ringtest - dierlijke eiwitten - analytische methoden - microscopie - visvoeding - diergezondheid - polymerase-kettingreactie
The annual ring test for the detection of animal proteins in animal feed of the IAG - International Association for Feeding stuff Analysis, Section Feeding stuff Microscopy was organized by RIKILT - Wageningen UR, The Netherlands. The aim of the ring study was to provide the participants information on the performance of the local implementation of the detection method for their local quality systems. A further aim was to gather information about the application of the microscopic method. The current 2016 version of the IAG ring test for animal proteins facilitated the full scenario with the methods for microscopy and PCR as published in Regulation (EC) 51/2013 amending Annex VI of Regulation (EC) 152/2009 together with accompanying SOPs. All four samples were based on an artificial feed mimicking a formulation for ruminant feed. Two samples were labelled as fish feed (B and D), which was effectuated by adding 2% of a general fish meal. Adulteration was achieved by adding 0.1% pig MBM (B), 0.1% ruminant MBM (D) and a combination of 0.1% ruminant MBM and 0.1% fish meal (C). This combination of different spikes allowed the diverse application of the detection methods. Forty eight participants enrolled for the ring test, of which 45 submitted microscopic results. Of these, 20 participants applied the combination of microscopic and PCR analysis. Three participants submitted exclusively PCR results.
DNA-diagnostiek maakt fytosanitaire controles beter en sneller : hightech gereedschap voor inspectie- en keuringsdiensten
Staalduinen, J. van; Bonants, P.J.M. - \ 2015
Onder Glas 12 (2015)6/7. - p. 48 - 49.
glastuinbouw - quarantaine organismen - detectie - technieken - innovaties - analytische methoden - fytosanitaire maatregelen - plantenplagen - polymerase-kettingreactie - landbouwkundig onderzoek - greenhouse horticulture - quarantine organisms - detection - techniques - innovations - analytical methods - phytosanitary measures - plant pests - polymerase chain reaction - agricultural research
Als vooraanstaand in- en exporteur van plantaardig uitgangsmateriaal en eindproducten heeft Nederland ook de taak om ongewenste organismen die met de handelswaar kunnen meereizen buiten of juist binnen de deur te houden. Wageningen UR ontwikkelt samen met partners in binnen- en buitenland nieuwe diagnose- en screeningsmethoden waarmee inspectie- en keuringsdiensten hun taken beter en efficiënter kunnen vervullen. DNA-analyse op de plaats van inspectie speelt daarin een belangrijke rol.
Offspring sex ratio bias and sex related characteristics of eggs in chicken
Aslam, M.A. - \ 2014
Wageningen University. Promotor(en): Mari Smits; T.G.G. Groothuis, co-promotor(en): Henri Woelders. - Wageningen : Wageningen University - ISBN 9789462570757 - 192
kippen - eieren - geslachtsverhouding - karakteristieken - nageslacht - toewijzing - polymerase-kettingreactie - hormonen - voedselbeperking - dierveredeling - fowls - eggs - sex ratio - characteristics - progeny - allocation - polymerase chain reaction - hormones - food restriction - animal breeding

Understanding the factors influencing sex of egg and sex ratio in laying chicken may lead to finding potential solutions for the problem of killing of day old male chicks, which is the current practice in breeding of laying hens. In studies described in this thesis, it was investigated if the sex of the chicken egg can be predicted by measurable differences in male and female eggs at unincubated stage and if the female primary sex ratio can be induced in laying chicken using different experimental conditions such as feed restriction and corticosterone feeding. The method of sex determination in unincubated chicken eggs using PCR targeted to CHD1 gene was first developed. This method was subsequently used to study the primary sex ratio bias as well as relationship between egg sex and yolk hormones. No significant relationship of the sex of egg with concentrations of several hormones (testosterone, estradiol, androstenedione, progesterone, dihydrotestosterone) and glucose in yolk as well as of egg parameters (mass, width and length) was found. Effect of feed availability on sex ratio was tested in two separate studies. In one study, the rate of change of hen body mass between day of laying and day of laying minus 2 days (encompass time of meiosis completion) was a significant predictor for the sex of that egg, suggesting meiotic drive as mechanism of sex ratio bias. This relationship was not found in the later study. The difference in results could be due to the reason that hens decreased in body mass much less in the later study as compared to earlier study. Blood corticosterone concentrations were associated with sex ratio per hen in the earlier study. Effect of egg mass on egg sex was studied during the later experiment of feed restriction. The egg sex ratio per hen was negatively associated with the average egg mass per hen in the feed restriction group. Two groups of hens were selected from the feed restriction group i.e. male biased hens with low egg mass and female biased hens with high egg mass for microarray analysis of gene expression in the germinal disc of collected F1 follicle. The results did not show differential expression of genes between the groups. However, gene set enrichment analysis showed that a number of processes related to cell cycle progression, mitotic/meiotic apparatus and chromosomal movement were differently enriched between the groups, supporting meiotic drive as potential mechanisms underlying sex ratio determination. In another experiment, blood circulating levels of corticosterone in hens were increased by feeding corticosterone mixed feed under ad libitum. The blood levels of corticosterone were significantly higher in treated hens but these levels were not associated with sex ratio. Treatment did not affect the overall sex ratio, but affected the sex ratio in interaction with hen body mass. In the corticosterone group, sex ratio, laying rate, and fertility rate per hen were decreased in heavy hens. These results suggest that three parameters (sex ratio, laying rate and fertility rate) are connected at the level of ovarian physiology. Interference with meiosis have been shown to affect these three parameters, suggesting the involvement of meiotic drive as mechanism of sex ratio bias.

Factsheet gebruik PlAMV-toetsen
Kock, M.J.D. de; Schadewijk, T. van; Frijlink, D. - \ 2012
lelies - lilium - kwaliteitscontroles - screenen - plantago asiatica mosaic virus - elisa - polymerase-kettingreactie - virusziekten - gewasbescherming - lilies - quality controls - screening - polymerase chain reaction - viral diseases - plant protection
Toetsen voor PlAMV zijn een onderdeel van een kwaliteitssysteem om virusvrij materiaal te produceren. Op basis van toetsuitslagen worden beslissingen gemaakt over de bestemming en gebruik van een partij. Het eerste overzicht met beschikbare toetsen voor PlAMV helpt bij het begrijpen van de verschillende toetsen die voor PlAMV beschikbaar zijn. In het tweede overzicht wordt per moment in de productiefase van lelies advies gegeven welke PlAMV-toetsen ingezet zouden moeten worden om met de grootst mogelijke betrouwbaarheid de virusstatus van een partij lelies te bepalen.
Vliegenpoepjesziekte in lelies : voortgezet diagnostisch onderzoek 2011
Vink, P. ; Pham, K.T.K. ; Kok, B.J. - \ 2011
Lisse : PPO Bloembollen en Bomen - 25
schimmelziekten - lilium - lelies - forceren van planten - polymerase-kettingreactie - diagnose - fungiciden - glastuinbouw - plantenziektebestrijding - bloembollen - snijbloemen - nederland - fungal diseases - lilies - forcing - polymerase chain reaction - diagnosis - fungicides - greenhouse horticulture - plant disease control - ornamental bulbs - cut flowers - netherlands
Bij de bloementeelt van lelies is in de herfst en wintermaanden soms sprake van veel economische schade doordat de waslaag van lelieplanten wordt aangetast door de schimmel Zygophiala. Daardoor ontstaan ongewenste stengelvlekken en een afwijkende bloemknopafrijping. In een consultancyproject is een beknopte literatuurstudie uitgevoerd over genoemde schimmel. Daarbij is vastgesteld dat de schimmel Zygophiala metname bij de teelt van appels in de USA en China het zogenaamde “flyspeck”kan veroorzaken. Ook andere gewassen met een duidelijke waslaag zoals anjers kunnen last hebben van een aantasting door deze schimmel. Uit zieke lelieplanten afkomstig uit Nederland zijn isolaties gemaakt en is met een geïsoleerde Zygophiala-schimmel een DNA-toets ontwikkeld. Daarmee is vanaf nu een snelle PCR-toets mogelijk om deze schimmel op en in lelieplanten aan te tonen. Ook is nagegaan wat de remmende werking is van een groot aantal, in Nederland gebruikte fungiciden op de schimmel Zygophiala . Het is gebleken dat een groot aantal van deze fungiciden zoals Allure, Ortiva, Mirage Plus, Kenbyo fl., Collis en Flint in vitro een goede remmende werking hebben tegen genoemde schimmel. Telers van lelies moeten daarmee in staat zijn om een aantasting door Zygophiala effectief te kunnen onderdrukken. Uit eerdere studies is gebleken dat het kasklimaat meestal een allesbepalende rol speelt bij problemen met Zygophiala. Daarom is het tevens van belang dat telers van lelies ook door middel van sturing van het kasklimaat proberen om een aantasting door deze schimmel te voorkomen.
Transmission dynamics of Eimeria acervulina in broilers
Velkers, F.C. - \ 2011
Wageningen University. Promotor(en): Mart de Jong; J.A. Stegeman, co-promotor(en): A. Bouma. - [S.l.] : S.n. - ISBN 9789085859215 - 153
vleeskuikens - eimeria acervulina - coccidiose - ziekteoverdracht - experimentele infectie - oöcysten - polymerase-kettingreactie - ziektebestrijding - vaccins - vaccinatie - epidemiologie - broilers - coccidiosis - disease transmission - experimental infection - oocysts - polymerase chain reaction - disease control - vaccines - vaccination - epidemiology

Control of the intestinal disease coccidiosis, caused by infections with Eimeria species, is a major challenge, especially for the broiler industry. Effective control strategies require a comprehensive understanding of processes that lead to infection and disease in a population. One of the key factors that determine infection dynamics in a flock is the rate of transmission between hosts. Therefore, transmission experiments were carried out to increase the understanding of the underlying mechanisms of Eimeria acervulina infections in broilers, to facilitate improvement of control strategies. An important outcome of the experiments was that the excreted oocyst dose, which may be related to severity of clinical signs, increased during successive generations of infection in the flock, but that the transmission rate was independent of the oocyst dose. This suggests that transmission is not determined by the number of oocysts excreted with faeces of infected birds but, most likely, by the probability of birds to come into contact with infectious faeces. Factors influencing the degree and dispersal of infectious faecal material in the environment, such as movements and (litter pecking) behaviour of chickens, environmental conditions and faeces characteristics, may have a large impact on infection dynamics and efficacy of control measures. Furthermore, it was demonstrated that a previous infection with a wild-type E. acervulina strain significantly reduced oocyst output and transmission after re-infection. After infection with a live vaccine strain, oocyst output following an infection with a wild-type strain was also significantly reduced. However, a significant reduction of transmission of the wild-type strain was not found in groups of broilers that had been infected with the vaccine strain. Nevertheless, it was demonstrated that the live vaccine was efficiently transmitted to initially unvaccinated birds. Furthermore, the level of reduction of oocyst output was equally high for directly vaccinated and the “contact-vaccinated” chickens, that became infected due to ingestion of oocysts excreted by vaccinated birds. These results indicate that transmission of the vaccine can induce protection against high oocyst output for the entire flock, even when not all birds receive the vaccine during the initial mass application. The results of these experiments indicate that influencing the rate of transmission of wild-type and vaccine strains can be important for reducing the adverse effects of flock infections with Eimeria. Furthermore, this thesis has increased insight into some of the underlying factors that determine transmission dynamics of E. acervulina in a broiler flock. Further investigation of these factors may reveal novel targets or facilitate improvement of current strategies for coccidiosis control.

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.
Vroegtijdig vuur detecteren kan bollentelers uit de brand helpen: identificatie en detectie van Botrytis-soorten in bloembolgewassen
Doorn, J. van; Pham, K.T.K. ; Kan, J.A.L. van - \ 2010
Gewasbescherming 41 (2010)5. - ISSN 0166-6495 - p. 219 - 222.
bloembollen - botrytis - detectie - versneld testen - polymerase-kettingreactie - vuur (plantenziektekundig) - schimmelsporen - luchtsporen - beslissingsondersteunende systemen - ornamental bulbs - detection - accelerated testing - polymerase chain reaction - blight - fungal spores - air spora - decision support systems
In bloembolgewassen kan de schimmel Botrytis veel schade veroorzaken. Botrytis kan snel toeslaan. Snelle en gevoelige toetsen kunnen dan bijdragen tot het op tijd nemen van maatregelen om ‘vuur’ te beheersen. Er komen verschillende Botrytis-soorten voor, die moleculair- genetisch gedetecteerd en geïdentificeerd kunnen worden. Serologische toetsen bleken niet te werken. PCR-methodieken, gebaseerd op enkele kleine verschillen in DNA-sequenties wel. Mogelijk kunnen via monitoring van luchtmonsters waarschuwingssystemen voor vuur verder worden verbeterd.
Bestrijding van fytoplasma's en kroeskoppen in rozen : eindrapportage 2006-2009
Smits, A.P. ; Kock, M.J.D. de; Meijer, H. ; Pham, K.T.K. - \ 2010
Lisse : PPO Bloembollen en Bomen - 60
afwijkingen, planten - rosa - rozen - phytoplasma - polymerase-kettingreactie - dna-sequencing - diagnostische technieken - landbouwkundig onderzoek - houtachtige planten als sierplanten - nederland - plant disorders - roses - polymerase chain reaction - dna sequencing - diagnostic techniques - agricultural research - ornamental woody plants - netherlands
Kroeskop is een al lang bekend verschijnsel in de rozenteelt waarbij geoculeerde rozen na ontspruiten van de oculatie dwerggroei en heksenbezemachtige groeiproblemen vertonen en een groot deel van de aangetaste planten sterft. Het pathogeen dat de aantasting veroorzaakt is een mysterie. Nieuwe detectietechnieken zoals de PCR-methode, DNA-sequentieanalyse en elektronmicroscopie hebben de laatste jaren een voor de wetenschap relatief nieuw organisme onthuld: het fytoplasma. Het fytoplasma is een celwandloze bacterie die in verband gebracht wordt met vele tot destijds onverklaarbare ziekten met vergelijkbare symptomen als kroeskop. Vanaf 2004 heeft PPO onderzoek uitgevoerd naar fytoplasma’s in rozen als mogelijke oorzaak van kroeskop. Hierbij werden al snel fytoplasma’s gevonden en gedetermineerd als een Aster Yellows fytoplasma. Aster Yellows is een groep van fytoplasma’s die bekend staan dat ze bij gewassen als aster en peen kroeskopachtige verschijnselen veroorzaken. Hoewel de fytoplasma’s als waarschijnlijke veroorzakers van kroeskoppen werden gezien, was het ultieme bewijs daarvoor nog niet geleverd. Binnen dit project is gekeken of de relatie tussen zieke planten en fytoplasma’s beter in beeld kon worden gebracht door te kijken naar: hoe de detectie van fytoplasma’s kan worden verbeterd, hoe de overdracht van fytoplasma’s plaatsvindt, hoe verspreid fytoplasma’s voorkomen in de Nederlandse rozenteelt, en wat de mogelijkheden zijn van bestrijding.
Snellere test voor ggo’s
Dijk, J.P. van - \ 2010
Kennis Online 7 (2010)juli. - p. 9 - 9.
voedselanalyse - transgene planten - diervoeding - polymerase-kettingreactie - testen - food analysis - transgenic plants - animal nutrition - polymerase chain reaction - testing
Met elk nieuw genetisch gemodificeerd gewas (ggo) dat ergens op een akker verschijnt, wordt het werk van analisten die voedingsmiddelen en diervoeders controleren een beetje ingewikkelder. Op RIKILT werkt Jeroen van Dijk aan een nieuw type test waarmee die analisten efficiënt hun werk kunnen blijven doen.
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 - 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.
Simultanema: Kwantitatieve simultane detectie van meerdere aaltjessoorten
Zijlstra, C. ; Hoof, R.A. van - \ 2009
plantenparasitaire nematoden - detectie - polymerase-kettingreactie - meloidogyne hapla - kwantitatieve methoden - plant parasitic nematodes - detection - polymerase chain reaction - quantitative methods
Poster met onderzoeksinformatie. Doel is een geschikte toets te maken voor de agrosector die snel, gelijktijdig meerdere aaltjessoorten kwantitatief kan aantonen.
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
Protocollering van toetsen op Erwinia
Dees, R.H.L. ; Martin, W.S. ; Doorn, J. van - \ 2009
Lisse : PPO Bloembollen en Bomen - 31
erwinia - dickeya chrysanthemi - elisa - polymerase-kettingreactie - diagnostische technieken - hyacinthus - dahlia - zantedeschia - iris (spermatophyta) - muscari - bloembollen - polymerase chain reaction - diagnostic techniques - ornamental bulbs
De problemen in de bloembollenteelt zijn de laatste tien jaar sterk toegenomen. Voorheen was de aanwezigheid van Erwinia carotovora subsp. carotovora (Ecc, nu Pectobacterium caotovorum) als witsnot in vooral hyacint bekend, maar gaf vrijwel nooit grote uitval in de teelt. Er zijn momenteel geen middelen om deze zachtrotbacteriën te bestrijden. Preventie via toetsing van vooral uitgangsmateriaal is een van de mogelijkheden om infectie met Erwinia vroegtijdig vast te stellen en verdere verspreiding in de keten te beperken. Daarom is de vraag vanuit de praktijk (telers, handelshuizen) naar toetsing van vooral hyacintenbollen op aanwezigheid van een infectie van Erwinia groot. Dickeya-soorten, voorheen Erwinia chrysanthemi (Ech), de veroorzaker van agressief snot geven op dit moment de grootste problemen voor de hyacintenteelt.
Toetsontwikkeling op virussen in Zantedeschia
Kock, M.J.D. de; Pham, K.T.K. ; Schadewijk, T. van; Miglino, R. - \ 2009
Lisse : PPO Bloembollen en Bomen (PPO rapport ) - 47
plantenvirussen - zantedeschia - polymerase-kettingreactie - elisa - diagnostische technieken - plantenziektebestrijding - bloembollen - landbouwkundig onderzoek - nederland - plant viruses - polymerase chain reaction - diagnostic techniques - plant disease control - ornamental bulbs - agricultural research - netherlands
Zantedeschia (=Calla) heeft zich ontwikkeld tot een belangrijk siergewas. Voor de productie van snijbloemen en potplanten is een goede kwaliteit vereist. Virus kan een sterk negatieve invloed hebben op de kwaliteit door o.a. groeimisvorming en kleurbreking op blad en bloem. Een kleine tien jaar geleden is de BKD op verzoek van het vak gestart met een keuring op o.a. zichtbaar virus. Sinds het groeiseizoen van 2003 zijn de virusproblemen ondanks de keuring alleen maar groter geworden. Het beperken van virusverspreiding in Zantedeschia is daarom recent in detail bestudeerd (PT-project 12048). Daarnaast is een goed toetsenpakket belangrijk om virusvrij uitgangsmateriaal te kunnen realiseren. Zonder robuuste toetsen op virussen in Zantedeschia is dit haast onmogelijk te verwezenlijken. Er zijn veel verschillende virussen gevonden in Zanedeschia en dit aantal is de afgelopen jaren verder gestegen. Een aantal virussen in Zanedeschia kan prima via serologische methoden als ELISA worden aangetoond; andere virussen alleen door middel van PCR. Voor sommige virussen in Zantedeschia waren bij de Bloembollenkeuringsdienst (BKD) en Praktijkonderzoek Plant en Omgeving (PPO-BBF) geen goede detectiemethoden aanwezig, of was bekend dat ze slecht met de bestaande toetsmethoden te detecteren zijn. Dit was een onbevredigende situatie, met name voor bedrijven die schoon uitgangsmateriaal willen uitleveren. Daarom heeft dit project als belangrijkste doel de kennis over virussen in Zantedeschia te vergroten en het pakket aan toetsmogelijkheden compleet te maken. De ELISA- en PCR-toetsen zijn binnen dit project gevalideerd met praktijkmateriaal en het protocol voor het toetsen op uitgangsmateriaal is geëvalueerd.
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