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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    Parasitism overrides herbivore identity allowing hyperparasitoids to locate their parasitoid host using herbivore-induced plant volatiles
    Zhu, F. ; Broekgaarden, C. ; Weldegergis, B.T. ; Harvey, J.A. ; Vosman, B. ; Dicke, M. ; Poelman, E.H. - \ 2015
    Molecular Ecology 24 (2015)1. - ISSN 0962-1083 - p. 2886 - 2899.
    cabbage brassica-oleracea - time rt-pcr - nicotiana-attenuata - insect herbivores - gene-expression - trophic levels - defense - responses - specialist - generalist
    Foraging success of predators profoundly depends on reliable and detectable cues indicating the presence of their often inconspicuous prey. Carnivorous insects rely on chemical cues to optimize foraging efficiency. Hyperparasitoids that lay their eggs in the larvae or pupae of parasitic wasps may find their parasitoid hosts developing in different herbivores. They can use herbivore-induced plant volatiles (HIPVs) to locate parasitized caterpillars. Because different herbivore species induce different HIPV emission from plants, hyperparasitoids may have to deal with large variation in volatile information that indicates host presence. In this study, we used an ecogenomics approach to first address whether parasitized caterpillars of two herbivore species (Pieris rapae and P. brassicae) induce similar transcriptional and metabolomic responses in wild Brassica oleracea plants and, second, whether hyperparasitoids Lysibia nana are able to discriminate between these induced plant responses to locate their parasitoid host in different herbivores under both laboratory and field conditions. Our study revealed that both herbivore identity and parasitism affect plant transcriptional and metabolic responses to herbivory. We also found that hyperparasitoids are able to respond to HIPVs released by wild B. oleracea under both laboratory and field conditions. In addition, we observed stronger attraction of hyperparasitoids to HIPVs when plants were infested with parasitized caterpillars. However, hyperparasitoids were equally attracted to plants infested by either herbivore species. Our results indicate that parasitism plays a major role in HIPV-mediated plant-hyperparasitoid interactions. Furthermore, these findings also indicate that plant trait-mediated indirect interaction networks play important roles in community-wide species interactions.
    Identification of reference genes for gene expression studies during seed germination and seedling establishment Ricinus communis L.
    Ribeiro de Jesus, P.R. ; Dekkers, S.J.W. ; Fernandez, L.G. ; Castro, R.D. De; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
    Seed Science Research 24 (2014)4. - ISSN 0960-2585 - p. 341 - 352.
    time rt-pcr - fatty-acid - jatropha-curcas - castor-oil - phosphoenolpyruvate carboxylase - arabidopsis - normalization - plant - cloning - family
    Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is an important technology to analyse gene expression levels during plant development or in response to different treatments. An important requirement to measure gene expression levels accurately is a properly validated set of reference genes. In this context, we analysed the potential use of 17 candidate reference genes across a diverse set of samples, including several tissues, different stages and environmental conditions, encompassing seed germination and seedling growth in Ricinus communis L. These genes were tested by RT-qPCR and ranked according to the stability of their expression using two different approaches: GeNorm and NormFinder. GeNorm and Normfinder indicated that ACT, POB and PP2AA1 comprise the optimal combination for normalization of gene expression data in inter-tissue (heterogeneous sample panel) studies. We also describe the optimal combination of reference genes for a subset of root, endosperm and cotyledon samples. In general, the most stable genes suggested by GeNorm are very consistent with those indicated by NormFinder, which highlights the strength of the selection of reference genes in our study. We also validated the selected reference genes by normalizing the expression levels of three target genes involved in energy metabolism with the reference genes suggested by GeNorm and NormFinder. The approach used in this study to identify stably expressed genes, and thus potential reference genes, was applied successfully for R. communis and it provides important guidelines for RT-qPCR studies in seeds and seedlings for other species (especially in those cases where extensive microarray data are not available)
    Tracing enteric viruses in the European berry fruit supply chain
    Maunula, L. ; Kaupke, A. ; Vasickova, P. ; Soderberg, K. ; Kozyra, I. ; Lazic, S. ; Poel, W.H.M. van der; Bouwknegt, M. ; Rutjes, S. ; Willems, K.A. ; Moloney, R. ; Agostino, M. D'; Husman, A.M.D. ; Bonsdorff, C.H. ; Rzezutka, A. ; Pavlik, I. ; Petrovic, T. ; Cook, N. - \ 2013
    International Journal of Food Microbiology 167 (2013)2. - ISSN 0168-1605 - p. 177 - 185.
    hepatitis-e virus - reverse transcription-pcr - time rt-pcr - waste-water - norovirus outbreaks - frozen raspberries - food safety - a virus - transmission - infection
    In recent years, numerous foodborne outbreaks due to consumption of berry fruit contaminated by human enteric viruses have been reported. This European multinational study investigated possible contamination routes by monitoring the entire food chain for a panel of human and animal enteric viruses. A total of 785 samples were collected throughout the food production chain of four European countries (Czech Republic, Finland, Poland and Serbia) during two growing seasons. Samples were taken during the production phase, the processing phase, and at point-of-sale. Samples included irrigation water, animal faeces, food handlers' hand swabs, swabs from toilets on farms, from conveyor belts at processing plants, and of raspberries or strawberries at points-of-sale; all were subjected to virus analysis. The samples were analysed by real-time (reverse transcription, RT)-PCR, primarily for human adenoviruses (hAdV) to demonstrate that a route of contamination existed from infected persons to the food supply chain. The analyses also included testing for the presence of selected human (norovirus, NoV GI, NoV GII and hepatitis A virus, HAV), animal (porcine adenovirus, pAdV and bovine polyomavirus, bPyV) and zoonotic (hepatitis E virus, HEV) viruses. At berry production, hAdV was found in 9.5%, 5.8% and 9.1% of samples of irrigation water, food handlers' hands and toilets, respectively. At the processing plants, hAdV was detected in one (2.0%) swab from a food handler's hand. At point-of-sale, the prevalence of hAdV in fresh raspberries, frozen raspberries and fresh strawberries, was 0.7%, 3.2% and 2.0%, respectively. Of the human pathogenic viruses, NoV GII was detected in two (3.6%) water samples at berry production, but no HAV was detected in any of the samples. HEV-contaminated frozen raspberries were found once (2.6%). Animal faecal contamination was evidenced by positive pAdV and bPyV assay results. At berry production, one water sample contained both viruses, and at point-of-sale 5.7% and 13% of fresh and frozen berries tested positive for pAdV. At berry production hAdV was found both in irrigation water and on food handler's hands, which indicated that these may be important vehicles by which human pathogenic viruses enter the berry fruit chain. Moreover, both zoonotic and animal enteric viruses could be detected on the end products. This study gives insight into viral sources and transmission routes and emphasizes the necessity for thorough compliance with good agricultural and hygienic practice at the farms to help protect the public from viral infections. (C) 2013 Elsevier B.V. All rights reserved.
    Predicted high-performing piglets exhibit more and larger skeletal muscle fibers
    Paredes Escobar, S.P. ; Kalbe, C. ; Jansman, A.J.M. ; Verstegen, M.W.A. ; Hees, H.M.J. van; Lösel, D. ; Gerrits, W.J.J. ; Rehfeldt, C. - \ 2013
    Journal of Animal Science 91 (2013)12. - ISSN 0021-8812 - p. 5589 - 5598.
    growth-factor system - meat quality traits - time rt-pcr - birth-weight - postnatal-growth - satellite cells - early gestation - messenger-rna - fetal growth - factor-ii
    Postnatal (muscle) growth potential in pigs depends on the total number and hypertrophy of myofibers in skeletal muscle tissue. In a previous study an algorithm was developed to predict piglet BW at the end of the nursery period (10 wk of age) on the basis of BW at birth, at weaning, and at 6 wk of age. The objective of this study was to determine whether the differences in growth performance between poor (PP) and high (HP) performing piglets could be the result of different skeletal muscle properties. Therefore, from a total of 368 piglets (offspring from Hypor sows bred to TOPIGS sires) 2 groups with a divergent growth performance were selected at 6 wk of age: HP (n = 20, predicted BW at 10 wk of age 26.8–30.9 kg) and PP (n = 20, predicted BW at 10 wk of age 16.0–22.9 kg). Piglets were euthanized at 10 wk of age, and samples of the semitendinosus muscle (STN) were collected for histochemistry and gene expression analysis using quantitative PCR (qPCR). At 10 wk of age, realized BW did not differ from predicted BW in either group (P > 0.880). The HP piglets exhibited greater ADG and ADFI from 6 to 10 wk and greater BW at birth and 6 and 10 wk of age (P = 0.002) compared with the PP piglets, whereas G:F ratio was similar (P = 0.417). Superior growth performance of HP piglets was associated with a 1.27-fold higher IGF1 plasma concentration at 10 wk compared with the PP piglets (P = 0.044). The greater weight and muscle cross-sectional area of STN in HP piglets was due to a 1.20-fold increase in total muscle fiber number (TFN; P = 0.009) and 1.34-fold increase in fiber cross-sectional area (FCSA; P = 0.004) compared with the PP piglets. The number of myonuclei per red and intermediate fiber was greater in HP piglets (P = 0.097), but the nucleus-to-cytoplasm ratio was unaffected by the performance group (P = 0.861). The mRNA expression of proliferating cell nuclear antigen (PCNA), paired box 7 (PAX7), myogenic factor 5 (MYF5), and myogenic differentiation factor (MYOD) did not differ between groups (P = 0.327). However, IGF2-specific mRNA expression was numerically higher in the HP piglets (P = 0.101). The greater myofiber number, the higher degree of myofiber hypertrophy, and the increased muscular mRNA expression of IGF2 indicate that HP piglets exhibit a greater capacity for lean accretion and may grow faster until market weight. In summary, pigs that were selected for predicted high BW at 10 wk of age using a complex selection model had a superior muscularity in terms of greater TFN and FCSA, which may be of advantage for lean mass accretion in later life and for meat quality.
    Rapid generation of replication-deficient monovalent and multivalent vaccines for bluetongue virus: protection against virulent virus challenge in cattle and sheep
    Celma, C.C.P. ; Boyce, M. ; Rijn, P.A. van; Eschbaumer, M. ; Wernike, K. ; Hoffmann, B. ; Beer, M. ; Clercq, K. De; Roy, P. - \ 2013
    Journal of Virology 87 (2013)17. - ISSN 0022-538X - p. 9856 - 9864.
    time rt-pcr - synthetic rna - particles - europe - vaccination - serotype-8 - strains - epidemic - proteins - efficacy
    Since 1998, nine of the 26 serotypes of bluetongue virus (BTV) have spread throughout Europe and serotype 8 has suddenly emerged in northern Europe causing considerable economic losses, both direct (mortality and morbidity) but also indirect due to restriction in animal movements. Therefore many new types of vaccines, particularly subunit vaccines, with improved safety and efficacy for a broad range of BTV serotypes are currently being developed by different laboratories. Here we exploited a reverse genetics-based replication-deficient BTV-1 serotype (disabled infectious single cycle, DISC) to generate a series of DISC vaccine strains. Cattle and sheep were vaccinated with these viruses either singly or in cocktail as multivalent vaccine candidate. All vaccinated animals were seroconverted and developed a neutralizing antibody response against their respective serotype. After challenge with the virulent strains at 21 days post vaccination vaccinated animals showed neither any clinical reaction nor viremia. Further, there was no interference in protection with a multivalent preparation of six distinct DISC viruses. These data indicate that a very rapid response vaccine could be developed based on which serotypes are circulating in the population at the time of an outbreak.
    Genome-wide gene expression analysis of anguillid herpesvirus 1
    Beurden, S.J. van; Peeters, B.P.H. ; Rottier, P.J.M. ; Davison, A.A. ; Engelsma, M.Y. - \ 2013
    BMC Genomics 14 (2013). - ISSN 1471-2164 - 11 p.
    channel catfish virus - time rt-pcr - dna microarray - european eel - murine gammaherpesvirus-68 - transcription - persistence - proteins - carp
    Background Whereas temporal gene expression in mammalian herpesviruses has been studied extensively, little is known about gene expression in fish herpesviruses. Here we report a genome-wide transcription analysis of a fish herpesvirus, anguillid herpesvirus 1, in cell culture, studied during the first 6 hours of infection using reverse transcription quantitative PCR. Results Four immediate-early genes – open reading frames 1, 6A, 127 and 131 – were identified on the basis of expression in the presence of a protein synthesis inhibitor and unique expression profiles during infection in the absence of inhibitor. All of these genes are located within or near the terminal direct repeats. The remaining 122 open reading frames were clustered into groups on the basis of transcription profiles during infection. Expression of these genes was also studied in the presence of a viral DNA polymerase inhibitor, enabling classification into early, early-late and late genes. In general, clustering by expression profile and classification by inhibitor studies corresponded well. Most early genes encode enzymes and proteins involved in DNA replication, most late genes encode structural proteins, and early-late genes encode non-structural as well as structural proteins. Conclusions Overall, anguillid herpesvirus 1 gene expression was shown to be regulated in a temporal fashion, comparable to that of mammalian herpesviruses.
    Virucidal efficacy of hydrogen peroxide vapour disinfection
    Tuladhar, E. ; Terpstra, P. ; Koopmans, M. ; Duizer, E. - \ 2012
    Journal of Hospital Infection 80 (2012)2. - ISSN 0195-6701 - p. 110 - 115.
    time rt-pcr - feline calicivirus - chemical disinfection - murine norovirus - decontamination - inactivation - surfaces - spread - contamination - environment
    Background: Viral contamination of surfaces is thought to be important in transmission. Chemical disinfection can be an effective means of intervention, but little is known about the virucidal efficacy of hydrogen peroxide vapour (HPV) against enteric and respiratory viruses. Aim: To measure the virucidal efficacy of HPV against respiratory and enteric viruses on materials representing those found in institutions and homes. Methods: Poliovirus, human norovirus genogroup II. 4 (GII. 4), murine norovirus 1, rotavirus, adenovirus and influenza A (H1N1) virus dried on to stainless steel, framing panel and gauze carriers were exposed to HPV 127 ppm for 1 h at room temperature in an isolator. Poliovirus was also exposed to HPV at different locations in a room. The virucidal effect was measured by comparing recoverable viral titres against unexposed controls. Polymerase chain reaction was used to evaluate the effect of HPV on viral genome reduction. Findings: HPV disinfection resulted in complete inactivation of all viruses tested, characterized by >4 log(10) reduction in infectious particles for poliovirus, rotavirus, adenovirus and murine norovirus on stainless steel and framing panel carriers, and >2 log(10) reduction for influenza A virus on stainless steel and framing panel carriers, and for all viruses on gauze carriers. Complete inactivation of poliovirus was demonstrated at several locations in the room. Reductions in viral genomes were minimal on framing panel and gauze carriers but significant on stainless steel carriers; human norovirus GII. 4 genome was most resistant to HPV treatment. Conclusion: HPV could be an effective virucidal against enteric and respiratory viruses contaminating in-house environments. (C) 2011 The Healthcare Infection Society.
    Virus hazards from food, water and other contaminated environments
    Rodriguez-Lázaro, D. ; Cook, N. ; Ruggeri, F.M. ; Sellwood, J. ; Nasser, A. ; Nascimento, M.S. ; Agostino, M. D'; Santos, R. ; Saiz, J.C. ; Rzezutka, A. ; Bosch, A. ; Girones, R. ; Carducci, A. ; Muscullo, M. ; Kovac, K. ; Diez-Valcarce, M. ; Vantarakis, A. ; Bonsdorff, C.H. ; Roda Husman, A.M. de; Hernández, M. ; Poel, W.H.M. van der - \ 2012
    FEMS Microbiology Reviews 36 (2012)4. - ISSN 0168-6445 - p. 786 - 814.
    hepatitis-e-virus - reverse transcription-pcr - human enteric viruses - polymerase-chain-reaction - norwalk-like virus - cell-culture-pcr - time rt-pcr - sequence-based amplification - human pathogenic viruses - treated drinking-water
    Numerous viruses of human or animal origin can spread in the environment and infect people via water and food, mostly through ingestion and occasionally through skin contact. These viruses are released into the environment by various routes including water run-offs and aerosols. Furthermore, zoonotic viruses may infect humans exposed to contaminated surface waters. Foodstuffs of animal origin can be contaminated, and their consumption may cause human infection if the viruses are not inactivated during food processing. Molecular epidemiology and surveillance of environmental samples are necessary to elucidate the public health hazards associated with exposure to environmental viruses. Whereas monitoring of viral nucleic acids by PCR methods is relatively straightforward and well documented, detection of infectious virus particles is technically more demanding and not always possible (e.g. human norovirus or hepatitis E virus). The human pathogenic viruses that are most relevant in this context are nonenveloped and belong to the families of the Caliciviridae, Adenoviridae, Hepeviridae, Picornaviridae and Reoviridae. Sampling methods and strategies, first-choice detection methods and evaluation criteria are reviewed.
    Comparative evaluation of live marker vaccine candidates "CP7_E2alf" and "flc11" along with C-strain "Riems" after oral vaccination
    Blome, S. ; Aebischer, A. ; Lange, E. ; Hofmann, M. ; Leifer, I. ; Loeffen, W.L.A. ; Koenen, F. ; Beer, M. - \ 2012
    Veterinary Microbiology 158 (2012)1-2. - ISSN 0378-1135 - p. 42 - 59.
    classical-swine-fever - time rt-pcr - e-rns - virus - pestiviruses - differentiation - pigs - e2
    Due to the tremendous socio-economic impact of classical swine fever (CSF) outbreaks, emergency vaccination scenarios are continuously under discussion. Unfortunately, all currently available vaccines show restrictions either in terms of marker capacities or immunogenicity. Recent research efforts were therefore directed at the design of new modified live marker vaccines. Among the most promising candidates the chimeric pestiviruses “CP7_E2alf” and “flc11” were identified. Within an international research project, these candidates were comparatively tested in challenge experiments after a single oral vaccination. Challenge infection was carried out with highly virulent CSF virus strain “Koslov”, 14 or 21 days post vaccination (dpv), respectively. Safety, efficacy, and marker potential were addressed. All assessments were done in comparison with the conventional “gold standard” C-strain “Riems” vaccine. In addition to the challenge trials, multiple vaccinations with both candidates were performed to further assess their marker vaccine potential. All vaccines were safe and yielded full protection upon challenge 21 days post vaccination. Neither serological nor virological investigations showed major differences among the three vaccines. Whereas CP7_E2alf also provided clinical protection upon challenge at 14 days post vaccination, only 50% of animals vaccinated with flc11, and 83% vaccinated with C-strain “Riems” survived challenge at this time point. No marked differences were seen in protected animals. Despite the fact that all multiple-vaccinated animals stayed sero-negative in the accompanying marker test, the discriminatory assay remains a weak point due to delayed or inexistent detection of some of the vaccinated and subsequently infected animals. Nevertheless, the potential as live marker vaccines could be confirmed for both vaccine candidates. Future efforts will therefore be directed at the licensing of “Cp7_E2alf” as the first live marker vaccine for CSF
    D-Xylose Concentration-Dependent Hydrolase Expression Profiles and the Function of CreA and XlnR in Aspergillus niger
    Mach-Aigner, A.R. ; Omony, J. ; Jovanovic, B. ; Boxtel, A.J.B. van; Graaff, L.H. de - \ 2012
    Applied and Environmental Microbiology 78 (2012)9. - ISSN 0099-2240 - p. 3145 - 3155.
    transcriptional activator xlnr - jecorina trichoderma-reesei - cell-wall polysaccharides - time rt-pcr - hypocrea-jecorina - encoding genes - xylanase expression - beta-xylosidase - enzyme-system - l-arabitol
    Aspergillus niger is an important organism for the production of industrial enzymes such as hemicellulases and pectinases. The xylan-backbone monomer, d-xylose, is an inducing substance for the coordinate expression of a large number of polysaccharide-degrading enzymes. In this study, the responses of 22 genes to low (1 mM) and high (50 mM) d-xylose concentrations were investigated. These 22 genes encode enzymes that function as xylan backbone-degrading enzymes, accessory enzymes, cellulose-degrading enzymes, or enzymes involved in the pentose catabolic pathway in A. niger. Notably, genes encoding enzymes that have a similar function (e.g., xylan backbone degradation) respond in a similar manner to different concentrations of d-xylose. Although low d-xylose concentrations provoke the greatest change in transcript levels, in particular, for hemicellulase-encoding genes, transcript formation in the presence of high concentrations of d-xylose was also observed. Interestingly, a high d-xylose concentration is favorable for certain groups of genes. Furthermore, the repressing influence of CreA on the transcription and transcript levels of a subset of these genes was observed regardless of whether a low or high concentration of d-xylose was used. Interestingly, the decrease in transcript levels of certain genes on high d-xylose concentrations is not reflected by the transcript level of their activator, XlnR. Regardless of the d-xylose concentration applied and whether CreA was functional, xlnR was constitutively expressed at a low level
    Analytical methods for virus detection in water and food
    Bosch, A. ; Sanchez, G. ; Abbaszadegan, M. ; Carducci, A. ; Guix, S. ; Guyader, F.S. Le; Netshikweta, R. ; Pintó, R.M. ; Poel, W.H.M. van der; Rutjes, S. ; Sano, D. ; Taylor, M.D. ; Zijl, W.B. Van; Rodriguez-Lázaro, D. ; Kovac, K. ; Sellwood, J. - \ 2011
    Food Analytical Methods 4 (2011)1. - ISSN 1936-9751 - p. 4 - 12.
    hepatitis-a-virus - sequence-based amplification - reverse transcription-pcr - time rt-pcr - polymerase-chain-reaction - monolithic chromatographic supports - human pathogenic viruses - acid extraction methods - treated drinking-water - enteric viruses
    Potential ways to address the issues that relate to the techniques for analyzing food and environmental samples for the presence of enteric viruses are discussed. It is not the authors’ remit to produce or recommend standard or reference methods but to address specific issues in the analytical procedures. Foods of primary importance are bivalve molluscs, particularly, oysters, clams, and mussels; salad crops such as lettuce, green onions and other greens; and soft fruits such as raspberries and strawberries. All types of water, not only drinking water but also recreational water (fresh, marine, and swimming pool), river water (irrigation water), raw and treated sewage are potential vehicles for virus transmission. Well over 100 different enteric viruses could be food or water contaminants; however, with few exceptions, most well-characterized foodborne or waterborne viral outbreaks are restricted to hepatitis A virus (HAV) and calicivirus, essentially norovirus (NoV). Target viruses for analytical methods include, in addition to NoV and HAV, hepatitis E virus (HEV), enteroviruses (e.g., poliovirus), adenovirus, rotavirus, astrovirus, and any other relevant virus likely to be transmitted by food or water. A survey of the currently available methods for detection of viruses in food and environmental matrices was conducted, gathering information on protocols for extraction of viruses from various matrices and on the various specific detection techniques for each virus type
    Expression profiling of functional genes in prenatal skeletal muscle tissue in Duroc and Pietrain pigs
    Davoli, R. ; Braglia, S. ; Russo, V. ; Varona, L. ; Pas, M.F.W. te - \ 2011
    Journal of Animal Breeding and Genetics 128 (2011)1. - ISSN 0931-2668 - p. 15 - 27.
    time rt-pcr - cyclin g1 - porcine fetal - sequence tags - family - protein - growth - cells - differentiation - cyclophilin
    In livestock, skeletal muscle is a tissue of major economic importance for meat production and muscle mass is largely determined during the prenatal period by the number and the size of muscle fibres. The understanding of gene expression changes during prenatal pig muscle development is still limited. In this study, genes identified as differentially expressed in a previous microarray research and chosen for the function of the coded protein as putative candidate involved in myogenesis were considered to analyse their expression profile during foetal growth of Duroc and Pietrain pigs. The eleven genes were considered by real-time PCR for a time-course evaluation of the transcription level at six stages of prenatal longissimus dorsi development. The results suggest that the most relevant variations in mRNA levels of the analysed genes seem to follow temporal waves of gene expression. Significant changes of transcription were observed at 21–35 and 63–91 days, the two main phases of skeletal muscle development. During the early phases of Pietrain embryos’ development, 10 of the 11 genes showed an induction. In Duroc embryos, a second phase of gene up-regulation can be identified in the phase 63–77 days. These results provide new data on developmental changes of expression profile of 11 genes involved in different functional pathways related to prenatal myogenic processes in Duroc and Pietrain pigs.
    Simulation modelling and risk assessment as tools to identify the impact of climate change on microbiological food safety – The case study of fresh produce supply chain
    Jacxsens, L. ; Luning, P.A. ; Vorst, J.G.A.J. van der; Devlieghere, F. ; Leemans, R. ; Uyttendaele, M. - \ 2010
    Food Research International 43 (2010)7. - ISSN 0963-9969 - p. 1925 - 1935.
    minimally processed vegetables - escherichia-coli o157-h7 - agricultural land-use - time rt-pcr - ambient-temperature - iceberg lettuce - cryptosporidium oocysts - foodborne pathogens - contaminated water - future scenarios
    The current quality assurance and control tools and methods to prevent and/or to control microbiological risks associated with fresh produce are challenged due to the following pressures upon the food supply chain, i.e. changing consumption patterns, globalization and climate change. It demonstrates the need for scientific research and development of new and/or improved tools, techniques and practices to adapt the current risk management systems. In this paper, a conceptual research approach is presented to analyse the complexity of the climate change and globalization challenge on the fresh produce supply chain taken as a case study. The factors which affect the vulnerability of the fresh produce chain demand a multidisciplinary research approach. The proposed knowledge-based modelling system is believed to be a most appropriate way to identify problems and to offer solutions to monitor and prevent microbiological food safety risks during all phases of food production and supply. To explore the potential impact of climate change and globalization, baseline information can be obtained by surveillance and performance measurement of implemented food safety management systems. Simulation of climate change scenarios and the logistic chain of fresh produce, along with mathematical models to optimize packaging technology to maintain quality and safety of fresh produce are tools to provide insights in the complex dynamic ecosystem. They are the basis for elaboration of risk assessment studies to scientifically support management options and decisions to new microbiological threats related to globalization and climate change in the fresh produce supply chain. This research concept as such will contribute to develop strategies in order to guarantee the (microbiological) food safety of fresh produce on the long term
    Analysis of variance components reveals the contribution of sample processing to transcript variation
    Veen, D. van der; Oliveira, J.M. ; Berg, W.A.M. van den; Graaff, L.H. de - \ 2009
    Applied and Environmental Microbiology 75 (2009)8. - ISSN 0099-2240 - p. 2414 - 2422.
    time rt-pcr - aspergillus-niger - gene-expression - microarray experiments - quantification - information - standards - nidulans - cloning - growth
    The proper design of DNA microarray experiments requires knowledge of biological and technical variation of the studied biological model. For the filamentous fungus Aspergillus niger, a fast, quantitative real-time PCR (qPCR)-based hierarchical experimental design was used to determine this variation. Analysis of variance components determined the contribution of each processing step to total variation: 68% is due to differences in day-to-day handling and processing, while the fermentor vessel, cDNA synthesis, and qPCR measurement each contributed equally to the remainder of variation. The global transcriptional response to d-xylose was analyzed using Affymetrix microarrays. Twenty-four statistically differentially expressed genes were identified. These encode enzymes required to degrade and metabolize D-xylose-containing polysaccharides, as well as complementary enzymes required to metabolize complex polymers likely present in the vicinity of D-xylose-containing substrates. These results confirm previous findings that the d-xylose signal is interpreted by the fungus as the availability of a multitude of complex polysaccharides. Measurement of a limited number of transcripts in a defined experimental setup followed by analysis of variance components is a fast and reliable method to determine biological and technical variation present in qPCR and microarray studies. This approach provides important parameters for the experimental design of batch-grown filamentous cultures and facilitates the evaluation and interpretation of microarray data
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