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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    Component-resolved microarray analysis of IgE sensitization profiles to Culicoides recombinant allergens in horses with insect bite hypersensitivity
    Novotny, Ella N. ; White, Samuel J. ; Wilson, A.D. ; Stefánsdóttir, Sara B. ; Tijhaar, Edwin ; Jonsdóttir, Sigridur ; Frey, Rebekka ; Reiche, Dania ; Rose, Horst ; Rhyner, Claudio ; Schüpbach-Regula, Gertraud ; Torsteinsdóttir, Sigurbjörg ; Alcocer, Marcos ; Marti, Eliane - \ 2020
    Allergy (2020). - ISSN 0105-4538
    culicoides allergens - equine insect bite hypersensitivity - IgE - microarray

    Background: Allergy to bites of blood-sucking insects, including biting midges, can affect both human and veterinary patients. Horses are often suffering from an IgE-mediated allergic dermatitis caused by bites of midges (Culicoides spp). With the aim to improve allergen immunotherapy (AIT), numerous Culicoides allergens have been produced as recombinant (r-) proteins. This study aimed to test a comprehensive panel of differently expressed Culicoides r-allergens on a cohort of IBH-affected and control horses using an allergen microarray. Methods: IgE levels to 27 Culicoides r-allergens, including 8 previously unpublished allergens, of which 11 were expressed in more than one expression system, were determined in sera from 347 horses. ROC analyses were carried out, cut-offs selected using a specificity of 95% and seropositivity rates compared between horses affected with insect bite hypersensitivity (IBH) and control horses. The combination of r-allergens giving the best performing test was determined using logistic regression analysis. Results: Seropositivity was significantly higher in IBH horses compared with controls for 25 r-allergens. Nine Culicoides r-allergens were major allergens for IBH with seven of them binding IgE in sera from > 70% of the IBH-affected horses. Combination of these top seven r-allergens could diagnose > 90% of IBH-affected horses with a specificity of > 95%. Correlation between differently expressed r-allergens was usually high (mean = 0.69, range: 0.28-0.91). Conclusion: This microarray will be a powerful tool for the development of component-resolved, patient-tailored AIT for IBH and could be useful for the study of allergy to biting midges in humans and other species.

    Photosynthetic response to increased irradiance correlates to variation in transcriptional response of lipid-remodeling and heat-shock genes
    Rooijen, Roxanne van; Harbinson, Jeremy ; Aarts, Mark G.M. - \ 2018
    Plant Direct 2 (2018)7. - ISSN 2475-4455
    Arabidopsis thaliana - high light stress - microarray - natural genetic variation - photosynthesis efficiency - photosystem II

    Plants have evolved several mechanisms for sensing increased irradiance, involving signal perception by photoreceptors (cryptochromes), and subsequent biochemical (reactive oxygen species, ROS) and metabolic clues to transmit the signals. This results in the increased expression of heat-shock response genes and of the transcription factor LONG HYPOCOTYL 5 (HY5, mediated by the cryptochrome photoreceptor 1, CRY1). Here, we show the existence of another response pathway in Arabidopsis. This pathway evokes the SPX1-mediated expression activation of the transcription factor PHR1 and leads to the expression of several galactolipid biosynthesis genes. Gene expression analysis of accessions Col-0, Ga-0, and Ts-1, showed activated expression of the SPX1/PHR1-mediated gene expression activation pathway acting on galactolipids biosynthesis genes in both Ga-0 and Col-0, but not in Ts-1. The activation of the SPX1/PHR1-mediated response pathway can be associated with lower photosynthesis efficiency in Ts-1, compared to Col-0 and Ga-0. Besides the accession-associated activation of the SPX1/PHR1-mediated response pathway, comparing gene expression in the accessions showed stronger activation of several heat responsive genes in Ga-0, and the opposite in Ts-1, when compared to Col-0, in line with the differences in their efficiency of photosynthesis. We conclude that natural variation in activation of both heat responsive genes and of galactolipids biosynthesis genes contribute to the variation in photosynthesis efficiency in response to irradiance increase.

    Childhood BMI in relation to microbiota in infancy and lifetime antibiotic use
    Korpela, K. ; Zijlmans, M.A.C. ; Kuitunen, M. ; Kukkonen, K. ; Savilahti, E. ; Salonen, A. ; Weerth, C. de; Vos, W.M. de - \ 2017
    University of Helsinki
    early-life microbiota - childhood overweight - Bifidobacteria - metabolic programming - microarray
    Background Children with high body mass index (BMI) at preschool age are at risk of developing obesity. Early identification of factors that increase the risk of excessive weight gain could help direct preventive actions. The intestinal microbiota and antibiotic use have been identified as potential modulators of early metabolic programming and weight development. To test if the early microbiota composition is associated with later BMI, and if antibiotic use modifies this association, we analysed the faecal microbiota composition at 3 months and the BMI at 5–6 years in two cohorts of healthy children born vaginally at term in the Netherlands (N = 87) and Finland (N = 75). We obtained lifetime antibiotic use records and measured weight and height of all children. Results The relative abundance of streptococci was positively and the relative abundance of bifidobacteria negatively associated with the BMI outcome. The association was especially strong among children with a history of antibiotic use. Bacteroides relative abundance was associated with BMI only in the children with minimal lifetime antibiotic exposure. Conclusions The intestinal microbiota of infants are predictive of later BMI and may serve as an early indicator of obesity risk. Bifidobacteria and streptococci, which are indicators of microbiota maturation in infants, are likely candidates for metabolic programming of infants, and their influence on BMI appears to depend on later antibiotic use.
    Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds
    Dou, Tengfei ; Zhao, Sumei ; Rong, Hua ; Gu, Dahai ; Li, Qihua ; Huang, Ying ; Xu, Zhiqiang ; Chu, Xiaohui ; Tao, Linli ; Liu, Lixian ; Ge, Changrong ; Pas, M.F.W. te; Jia, Junjing - \ 2017
    Yunnan Agriculture University
    growth rate - chicken breeds - Gallus gallus - breast muscle - liver - microarray - metabolic differences - biological mechanisms
    Background Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. Results The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. Conclusions We conclude that faster growth rates and larger body size are related to increased expression of genes involved in muscle development and immune response in muscle, while slower growth rates and smaller body size are related to increased general cellular metabolism. The liver of the Daweishan breed displayed increased expression of metabolic genes.
    Effects of selective digestive decontamination (SDD) on the gut resistome
    Buelow, E. ; Bello Gonzalez, T.D.G. ; Versluis, D. ; Oostdijk, E.A.N. ; Ogilvie, L.A. ; Mourik, M.S.M. van; Oosterink, L. ; Passel, M.W.J. van; Smidt, H. ; D’Andrea, M.M. ; Been, M. de; Jones, B.V. ; Willems, R.J.L. ; Bonten, M.J.M. ; Schaik, W. - \ 2014
    Journal of Antimicrobial Chemotherapy 69 (2014)8. - ISSN 0305-7453 - p. 2215 - 2223.
    intensive-care units - antimicrobial resistance - microbiota - tract - microarray - metagenome - sequences - bacterial - classification - generation
    Objectives Selective digestive decontamination (SDD) is an infection prevention measure for critically ill patients in intensive care units (ICUs) that aims to eradicate opportunistic pathogens from the oropharynx and intestines, while sparing the anaerobic flora, by the application of non-absorbable antibiotics. Selection for antibiotic-resistant bacteria is still a major concern for SDD. We therefore studied the impact of SDD on the reservoir of antibiotic resistance genes (i.e. the resistome) by culture-independent approaches. Methods We evaluated the impact of SDD on the gut microbiota and resistome in a single ICU patient during and after an ICU stay by several metagenomic approaches. We also determined by quantitative PCR the relative abundance of two common aminoglycoside resistance genes in longitudinally collected samples from 12 additional ICU patients who received SDD. Results The patient microbiota was highly dynamic during the hospital stay. The abundance of antibiotic resistance genes more than doubled during SDD use, mainly due to a 6.7-fold increase in aminoglycoside resistance genes, in particular aph(2¿)-Ib and an aadE-like gene. We show that aph(2¿)-Ib is harboured by anaerobic gut commensals and is associated with mobile genetic elements. In longitudinal samples of 12 ICU patients, the dynamics of these two genes ranged from a ~104 fold increase to a ~10-10 fold decrease in relative abundance during SDD. Conclusions ICU hospitalization and the simultaneous application of SDD has large, but highly individualized, effects on the gut resistome of ICU patients. Selection for transferable antibiotic resistance genes in anaerobic commensal bacteria could impact the risk of transfer of antibiotic resistance genes to opportunistic pathogens.
    Alteration of gene expression in mammary gland tissue of dairy cows in response to dietary unsaturated fatty acids
    Mach Casellas, N. ; Jacobs, A.A.A. ; Kruijt, L. ; Baal, J. van; Smits, M.C.J. - \ 2014
    animal nutrition and feeding - diary cow - Mammary gland - microarray - unsaturated fatty acids - GSE20909 - PRJNA124449
    The aim of this study was to determine the effects of unprotected dietary unsaturated fatty acids (UFA) from different plant oils on gene expression in the mammary gland of grazing dairy cows. Milk composition and gene expression in the mammary gland tissue were evaluated in grazing dairy cows supplemented with different unsaturated fatty acids (UFA). The UFA supplementation improves the health and nutrition quality aspects of dairy milk, but also affects the gene networks expression signature associated with cellular growth and proliferation, cell-death, signalling, nutrient metabolism, and immune response, and in turn, the mammary gland integrity and health. SUBMITTER_CITATION: Mach, N., A. A. A. Jacobs, L. Kruijt, J. Van Baal, and M. A. Smits. 2011. Alteration of gene expression in mammary gland tissue of dairy cows in response to dietary unsaturated fatty acids. Animal.DOI:10.1017/S1751731111000103
    Short term, high fat-feeding induced changes in white adipose tissue gene expression are highly predictive for long term changes
    Voigt, A. ; Agnew, K. ; Schothorst, E.M. van; Keijer, J. ; Klaus, S. - \ 2013
    Molecular Nutrition & Food Research 57 (2013)8. - ISSN 1613-4125 - p. 1423 - 1434.
    diet-induced obesity - epigallocatechin gallate - uncoupling protein-1 - insulin-resistance - mice - microarray - oxidation - efficiency - adipocytes - alpha
    Scope - We aimed to evaluate the predictability of short-term (5 days) changes in epididymal white adipose tissue (eWAT) gene expression for long-term (12 weeks) changes induced by high-fat diet (HFD) feeding. Methods and results - Mice were fed semisynthetic diets containing 10 (low-fat diet) or 40 (HFD) energy% of fat. Global gene expression in eWAT was analyzed using microarrays and confirmed by quantitative PCR. As expected, HFD feeding resulted in increased body fat accumulation and reduced glucose tolerance after 12 weeks. A total of 4678 transcripts were significantly changed by HFD after 12 weeks and 973 after 5 days, with an overlap of 764 transcripts encoding 549 genes. Of these, 79% were downregulated and 21% were upregulated by HFD, all in the same direction and highly correlated (r2 = 0.90) between the time points. Pathway analysis showed downregulation of the main identified processes: lipid metabolism, carbohydrate metabolism, and oxidative phosphorylation. Mest (mesoderm-specific transcript) was highly upregulated, confirming its role as an early marker of fat cell expansion. Conclusion - The high predictive value of short-term gene expression changes for long-term effects of high fat feeding is a promising step to establish robust early biomarkers that could shorten animal trials to assess health-promoting food compounds.
    Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review
    Lahti, L.M. ; Schäfer, M. ; Klein, H.U. ; Bicciato, S. ; Dugas, M. - \ 2013
    Briefings in Bioinformatics 14 (2013)1. - ISSN 1467-5463 - p. 27 - 35.
    canonical correlation-analysis - acute lymphoblastic-leukemia - breast-cancer - r-package - genomic data - microarray - aberrations - regression - pathways - impact
    A variety of genome-wide profiling techniques are available to investigate complementary aspects of genome structure and function. Integrative analysis of heterogeneous data sources can reveal higher level interactions that cannot be detected based on individual observations. A standard integration task in cancer studies is to identify altered genomic regions that induce changes in the expression of the associated genes based on joint analysis of genome-wide gene expression and copy number profiling measurements. In this review, we highlight common approaches to genomic data integration and provide a transparent benchmarking procedure to quantitatively compare method performances in cancer gene prioritization. Algorithms, data sets and benchmarking results are available at http://intcomp.r-forge.r-project.org
    The Influence of Long-Term Copper Contaminated Agricultural Soil at Different pH Levels on Microbial Communities and Springtail Transcriptional Regulation
    Boer, T.E. de; Tas, N. ; Braster, M. ; Temminghoff, E.J.M. ; Roling, W.F.M. ; Roelofs, D. - \ 2012
    Environmental Science and Technology 46 (2012)1. - ISSN 0013-936X - p. 60 - 68.
    heavy-metal contamination - bacterial community - organic status - fungal communities - arable soil - sandy soil - diversity - toxicity - microorganisms - microarray
    Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block. design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology.
    Gene expression patterns in the ventral tegmental area relate to oestrus behaviour in high-producing dairy cows
    Wyszynska-Koko, J. ; Wit, A.A.C. de; Beerda, B. ; Veerkamp, R.F. ; Pas, M.F.W. te - \ 2011
    Journal of Animal Breeding and Genetics 128 (2011)3. - ISSN 0931-2668 - p. 183 - 191.
    cerebral-cortex - immunoglobulin - fertility - normalization - microarray - molecules - profiles - adhesion - neurons - stress
    Reduced oestrus behaviour expression or its absence (silent oestrus) results in subfertility in high-producing dairy cows. Insight into the genomic regulation of oestrus behaviour is likely to help alleviate reproduction problems. Here, gene expression was recorded in the ventral tegmental area (VTA) of high milk production dairy cows differing in the degree of showing oestrus behaviour (H – highly expressing versus L – lowly expressing), which was then analysed. Genes regulating cell morphology and adhesion or coding for immunoglobulin G (IgG) chains were differentially expressed in VTA between cows around day 0 and 12 of the oestrus cycle, but only in cows that earlier in life tended to show high levels of oestrus behaviour (H0 versus H12). The comparisons between H and L groups of cows also revealed differential expression of several genes (e.g. those of the IgG family or encoding for pro-melanin-concentrating hormone). However, any significant changes in VTA genes expression were detected in the comparison of L0 versus L12 cows. Altogether, the genes expression profile in VTA of cows highly expressing oestrus behaviour changes together with phases of the oestrus cycle, while in case of cows expressing oestrus behaviour lowly it remains stable. This supports the existence of genomic regulation by centrally expressed genes on the expression of oestrus behaviour in dairy cows.
    PVYNTN elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation
    Baebler, S. ; Krecic-Stres, H. ; Rotter, A. ; Kogovsek, P. ; Cankar, K. ; Kok, E.J. ; Gruden, K. ; Kovac, M. ; Zel, J. ; Pompe-Novak, M. ; Ravnikar, M. - \ 2009
    Molecular Plant Pathology 10 (2009)2. - ISSN 1464-6722 - p. 263 - 275.
    mosaic-virus-infection - arabidopsis-thaliana - cysteine proteinases - real-time - y-ntn - resistance - tobacco - defense - plants - microarray
    Host gene expression changes in the early response to potato virus Y-NTN interaction were compared in two differently sensitive potato cultivars: the resistant cultivar SantE and the sensitive cultivar Igor. Hybridization of potato TIGR cDNA microarrays allowed us to monitor the expression of approximately 10 000 genes simultaneously at 0.5 and 12 h post-inoculation (hpi). Microarray data, analysed by statistics and data mining, were complemented by subtraction library construction and sequence analysis to validate the findings. The expression profiles of the two cultivars were similar and faint at 0.5 hpi, but they differed substantially at 12 hpi. Although, at 0.5 hpi, cv. SantE responded by the differential expression of a greater number of genes, at 12 hpi the number was higher in cv. Igor. The majority of genes in this cultivar were down-regulated at 12 hpi, indicating a host gene shut-off. Suites of genes that exhibited altered transcript abundance in response to the virus were identified, and included genes involved in the processes of photosynthesis, perception, signalling and defence responses. The expression of the considerable number of genes associated with photosynthesis was surprisingly up-regulated as early as 0.5 hpi and down-regulated at 12 hpi in both cultivars. The expression of genes involved in perception and signalling was increased in the sensitive cultivar at 12 hpi. By contrast, a simultaneous strong defence response at the transcriptional level was evident in the resistant cultivar, as shown by the up-regulation of genes involved in brassinosteroid, polyamine and secondary metabolite biosynthesis, and of genes coding for pathogenesis-related proteins.
    Suitability of Rapid Detection Methods for Salmonella in Poultry Slaughterhouses
    Eijkelkamp, J.M. ; Aarts, H.J.M. ; Fels-Klerx, H.J. van der - \ 2009
    Food Analytical Methods 2 (2009)1. - ISSN 1936-9751 - p. 1 - 13.
    antibiotic-resistance genes - polymerase-chain-reaction - real-time pcr - food - validation - microarray - microorganisms - biosensors - standard - samples
    In the perspective of an announced prohibition to bring Salmonella-contaminated fresh poultry meat on the retail market as of December 2010, requirements are postulated for rapid methods for detection of Salmonella in poultry meat. These rapid methods should deliver reliable results in time to make it possible to steer the finished products in poultry slaughterhouses into the direction of the fresh poultry market or into the direction of industrial treatment. The most important requirements are the detection limit (1 cfu/25 g), the time of analysis (within hours up to a maximum of 24 h), the sensitivity and specificity, and the validation of the rapid detection method. To determine a requirement for the number of samples to be analyzed per unit of time of the detection methods, a sampling plan for pooling of samples is suggested. Information of commercially available detection methods from literature and data provided by the suppliers was compared to the postulated requirements. The results showed that none of the commercially available detection methods meet all the suggested requirements. For all available methods, the time of analysis is too long to steer the production process in time. This implicates that faster methods should be developed before the announced prohibition can be sensibly introduced. Also, information about sensitivity and specificity, which is essential for the reliability of the rapid test method, should be examined in a more uniform way
    Transcriptome Analysis of Potato Tubers - Effects of Different Agricultural Practices
    Dijk, J.P. van; Cankar, K. ; Scheffer, S.J. ; Beenen, H.G. ; Shepherd, L.V.T. ; Stewart, D. ; Davies, H.V. ; Wilkockson, S.J. ; Leifert, C. ; Gruden, K. ; Kok, E.J. - \ 2009
    Journal of Agricultural and Food Chemistry 57 (2009)4. - ISSN 0021-8561 - p. 1612 - 1623.
    gene-expression - immunocytochemical localization - proteinase-inhibitors - enzyme-inhibitors - molecular-cloning - microarray - family - safety - foods - glucosyltransferase
    The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments.
    Challenges in plant cellular pathway reconstruction based on gene expression profiling
    Baarlen, P. van; Esse, H.P. van; Siezen, R.J. ; Thomma, B.P.H.J. - \ 2008
    Trends in Plant Science 13 (2008)1. - ISSN 1360-1385 - p. 44 - 50.
    arabidopsis-thaliana - reconciled trees - data sets - death - database - microarray - network - identification - orthologs - model
    Microarrays are used to profile transcriptional activity, providing global cell biology insight. Particularly for plants, interpretation of transcriptional profiles is challenging because many genes have unknown functions. Furthermore, many plant gene sequences do not have clear homologs in other model organisms. Fortunately, over the past five years, various tools that assist plant scientists have been developed. Here, we evaluate the currently available in silico tools for reconstruction of cellular (metabolic, biochemical and signal transduction) pathways based on plant gene expression datasets. Furthermore, we show how expression-profile comparison at the level of these various cellular pathways contributes to the postulation of novel hypotheses which, after experimental verification, can provide further insight into decisive elements that have roles in cellular
    Nutrigenomic approaches for benefit-risk analysis of foods and food components:defining markers of health
    Elliott, R. ; Pico, C. ; Dommels, Y.E.M. ; Wybranska, I. ; Hesketh, J. ; Keijer, J. - \ 2007
    The British journal of nutrition 98 (2007)6. - ISSN 0007-1145 - p. 1095 - 1100.
    gene set enrichment - caloric restriction - expression profiles - human blood - transcriptome - humans - microarray - responses - pathways - protein
    To be able to perform a comprehensive and rigorous benefit-risk analysis of individual food components, and of foods, a number of fundamental questions need to be addressed first. These include whether it is feasible to detect all relevant biological effects of foods and individual food components, how such effects can confidently be categorised into benefits and risks in relation to health and, for that matter, how health can be quantified. This article examines the last of these issues, focusing upon concepts for the development of new biomarkers of health. Clearly, there is scope for refinement of classical biomarkers so that they may be used to detect even earlier signs of disease, but this approach defines health solely as the absence of detectable disease or disease risk. We suggest that the health of a biological system may better be reflected by its ability to withstand and manage relevant physiological challenges so that homeostasis is maintained. We discuss the potential for expanding the range of current challenge tests for use in conjunction with functional genomic technologies to develop new types of biomarkers of health.
    Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
    Kiekens, R. ; Vercauteren, A. ; Moerkerke, B. ; Goetghebeur, E. ; Daele, H. Van Den; Sterken, R. ; Kuiper, M. ; Eeuwijk, F.A. van; Vuylsteke, M. - \ 2006
    Nucleic acids research 34 (2006)13. - ISSN 0305-1048 - p. 3677 - 3686.
    human gene-expression - allelic variation - transcriptional regulation - arabidopsis-thaliana - functional genomics - sequence tags - microarray - model - identification - construction
    Large-scale screening studies carried out to date for genetic variants that affect gene regulation are generally limited to descriptions of differences in allele-specific expression (ASE) detected in vivo. Allele-specific differences in gene expression provide evidence for a model whereby cis-acting genetic variation results in differential expression between alleles. Such gene surveys for regulatory variation are a first step in identifying the specific nucleotide changes that govern gene expression differences, but they leave the underlying mechanisms unexplored. Here, we propose a quantitative genetics approach to perform a genome-wide analysis of ASE differences (GASED). The GASED approach is based on a diallel design that is often used in plant breeding programs to estimate general combining abilities (GCA) of specific inbred lines and to identify high-yielding hybrid combinations of parents based on their specific combining abilities (SCAs). In a context of gene expression, the values of GCA and SCA parameters allow cis- and trans-regulatory changes to be distinguished and imbalances in gene expression to be ascribed to cis-regulatory variation. With this approach, a total of 715 genes could be identified that are likely to carry allelic polymorphisms responsible for at least a 1.5-fold allelic expression difference in a total of 10 diploid Arabidopsis thaliana hybrids. The major strength of the GASED approach, compared to other ASE detection methods, is that it is not restricted to genes with allelic transcript variants. Although a false-positive rate of 9/41 was observed, the GASED approach is a valuable pre-screening method that can accelerate systematic surveys of naturally occurring cis-regulatory variation among inbred lines for laboratory species, such as Arabidopsis, mouse, rat and fruitfly, and economically important crop species, such as corn.
    Comparative transcriptomics - model species lead the way.
    Mortel, J.E. van de; Aarts, M.G.M. - \ 2006
    New Phytologist 170 (2006)2. - ISSN 0028-646X - p. 199 - 201.
    arabidopsis-thaliana - microarray - expression - genes - genomics - halleri
    Evaluation of a non-targeted "omic" approach in the safety assessment of genetically modified plants
    Metzdorff, S.B. ; Kok, E.J. ; Knuthsen, P. ; Pedersen, J. - \ 2006
    Plant Biology 8 (2006). - ISSN 1435-8603 - p. 662 - 672.
    t-dna integration - arabidopsis-thaliana - expression - gene - light - microarray - suggest - complex - protein - potato
    Genetically modified plants must be approved before release in the European Union, and the approval is generally based upon a comparison of various characteristics between the transgenic plant and a conventional counterpart. As a case study, focusing on safety assessment of genetically modified plants, we here report the development and characterisation of six independently transformed Arabidopsis thaliana lines modified in the flavonoid biosynthesis. Analyses of integration events and comparative analysis for characterisation of the intended effects were performed by PCR, quantitative Real-time PCR, and High Performance Liquid Chromatography. Analysis by cDNA microarray was used as a non-targeted approach for the identification of potential unintended effects caused by the transformation. The results revealed that, although the transgenic lines possessed different types of integration events, no unintended effects were identified. However, we found that the majority of genes showing differential expression were identified as stress-related genes and that environmental conditions had a large impact on the expression of several genes, proteins, and metabolites. We suggest that the microarray approach has the potential to become a useful tool for screening of unintended effects, but state that it is crucial to have substantial information on the natural variation in traditional crops in order to be able to interpret ¿omics¿ data correctly within the framework of food safety assessment strategies of novel plant varieties, including genetically modified plant varieties
    Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates
    Hermans, A.P.H.M. ; Beuling, A.M. ; Hoek, A.H.A.M. van; Aarts, H.J.M. ; Abee, T. ; Zwietering, M.H. - \ 2006
    Microbiology 152 (2006)7. - ISSN 1350-0872 - p. 2137 - 2147.
    complete genome sequence - molecular characterization - phage types - bacteriophage - dt104 - identification - microarray - evolution - virulence - epidemic
    Recently, the authors identified Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive type (DT)104-specific sequences of mainly prophage origin by genomic subtractive hybridization. In the present study, the distribution of the prophages identified, ST104 and ST64B, and the novel prophage remnant designated prophage ST104B, was tested among 23 non-DT104 S. Typhimurium isolates of different phage types and 19 isolates of the DT104 subtypes DT104A, DT104B low and DT104L, and the DT104-related type U302. The four S. Typhimurium prophages Gifsy-1, Gifsy-2, Fels-1 and Fels-2 were also included. Analysis of prophage distribution in different S. Typhimurium isolates may supply additional information to enable development of a molecular method as an alternative to phage typing. Furthermore, the presence of the common DT104 antibiotic resistance genes for the penta-resistance type ACSSuT, aadA2, floR, pse-1, sul1 and tet(G), was also studied because of the authors' focus on this emerging type. Based on differences in prophage presence within their genome, it was possible to divide S. Typhimurium isolates into 12 groups. Although no clear relationship was found between different phage type and prophage presence, discrimination could be made between the different DT104 subtypes based on diversity in the presence of prophages ST104, ST104B and ST64B. The novel prophage remnant ST104B, which harbours a homologue of the Escherichia coli O157 : H7 HldD LPS assembly-related protein, was identified only in the 14 DT104L isolates and in the DT104-related U302 isolate. In conclusion, the presence of the genes for penta-resistance type ACSSuT, the HldD homologue containing ST104 prophage remnant and phage type DT104L are most likely common features of the emerging subtype of S. Typhimurium DT104.
    Detecting single nucleotide polymorphisms using DNA arrays for plant pathogen diagnosis
    Lievens, B. ; Claes, L. ; Vanachter, A.C.R.C. ; Cammue, B.P.A. ; Thomma, B.P.H.J. - \ 2006
    FEMS Microbiology Letters 255 (2006)1. - ISSN 0378-1097 - p. 129 - 139.
    dot-blot hybridization - wilt pathogens - identification - differentiation - microarray - phytophthora - potato
    The lack of a rapid and reliable means for routine pathogen identification has been one of the main limitations in plant disease management, and has pushed the development of culture-independent, molecular approaches. Currently, DNA array technology is the most suitable technique for high-throughput detection and identification, as well as quantification, of multiple pathogens in a single assay. Closely related pathogens that may have completely different host ranges or pathogenicity often differ in only a single to a few base pairs in genes that may be targeted for identification. Therefore, the ability to discriminate single nucleotide polymorphisms (SNPs) should be pursued in any diagnostic assay. In this paper, we demonstrate the utility of DNA array technology to detect SNPs while accounting for specific criteria such as the position of the mismatch, the sequence of the oligonucleotide, and the length and amount of labeled amplicons that are hybridized. When disregarding mismatches at the extreme ends of the oligonucleotides, cross hybridization to single mismatch oligonucleotides is rare when processing environmental samples that contain genetic material from unknown sources. In addition to plant pathology, this study is relevant for any field of research where DNA arrays are used to detect mutations or polymorphisms, ranging from human diagnostics to environmental microbiology and microbial ecology.
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