Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    '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.

    We have a manual that explains all the features 

Current refinement(s):

Records 21 - 31 / 31

  • help
  • print

    Print search results

  • export

    Export search results

  • alert
    We will mail you new results for this query: keywords==Gene expression
Check title to add to marked list
A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation
Velpen, V. van der; Veer, P. van 't; Islam, M.A. ; Braak, C.J.F. ter; Leeuwen, F.X.R. ; Afman, L.A. ; Hollman, P.C.H. ; Schouten, A. ; Geelen, M.M.E.E. - \ 2016
Food and Chemical Toxicology 95 (2016). - ISSN 0278-6915 - p. 203 - 210.
Risk assessment - Gene expression - Species and tissue differences - Quantitative evaluation - Isoflavones - Multivariate model
Quantitative insight into species differences in risk assessment is expected to reduce uncertainty and variability related to extrapolation from animals to humans. This paper explores quantification and comparison of gene expression data between tissues and species from intervention studies with isoflavones.

Gene expression data from peripheral blood mononuclear cells (PBMCs) and white adipose tissue (WAT) after 8wk isoflavone interventions in postmenopausal women and ovariectomized F344 rats were used. A multivariate model was applied to quantify gene expression effects, which showed 3–5-fold larger effect sizes in rats compared to humans. For estrogen responsive genes, a 5-fold greater effect size was found in rats than in humans. For these genes, intertissue correlations (r = 0.23 in humans, r = 0.22 in rats) and interspecies correlation in WAT (r = 0.31) were statistically significant. Effect sizes, intertissue and interspecies correlations for some groups of genes within energy metabolism, inflammation and cell cycle processes were significant, but weak.

Quantification of gene expression data reveals differences between rats and women in effect magnitude after isoflavone supplementation. For risk assessment, quantification of gene expression data and subsequent calculation of intertissue and interspecies correlations within biological pathways will further strengthen knowledge on comparability between tissues and species.
Differences in genome-wide gene expression response in peripheral blood mononuclear cells between young and old men upon caloric restriction
Bussel, I.P.G. van; Jolink-Stoppelenburg, J.A. ; Groot, C.P.G.M. de; Müller, M.R. ; Afman, L.A. - \ 2016
Genes & Nutrition 11 (2016). - ISSN 1555-8932
Age - Caloric restriction - Gene expression - Microarray - Peripheral blood mononuclear cells

Background: Caloric restriction (CR) is considered to increase lifespan and to prevent various age-related diseases in different nonhuman organisms. Only a limited number of CR studies have been performed on humans, and results put CR as a beneficial tool to decrease risk factors in several age-related diseases. The question remains at what age CR should be implemented to be most effective with respect to healthy aging. The aim of our study was to elucidate the role of age in the transcriptional response to a completely controlled 30 % CR diet on immune cells, as immune response is affected during aging. Ten healthy young men, aged 20-28, and nine healthy old men, aged 64-85, were subjected to a 2-week weight maintenance diet, followed by 3 weeks of 30 % CR. Before and after 30 % CR, the whole genome gene expression in peripheral blood mononuclear cells (PBMCs) was assessed. Results: Expression of 554 genes showed a different response between young and old men upon CR. Gene set enrichment analysis revealed a downregulation of gene sets involved in the immune response in young but not in old men. At baseline, immune response-related genes were higher expressed in old compared to young men. Upstream regulator analyses revealed that most potential regulators were controlling the immune response. Conclusions: Based on the gene expression data, we theorise that a short period of CR is not effective in old men regarding immune-related pathways while it is effective in young men.

Supplementation of piglets with nutrient-dense complex milk replacer improves intestinal development and microbial fermentation
Greeff, A. de; Resink, J.W. ; Hees, H.M.J. van; Ruuls, L. ; Klaassen, G.J. ; Rouwers, S.M.G. ; Stockhofe-Zurwieden, N. - \ 2016
Journal of Animal Science 94 (2016)3. - ISSN 0021-8812 - p. 1012 - 1019.
Circular intestinal growth - Gene expression - Gut health - Nutrient-dense complex milk replacer - Pig

Weaning of piglets causes stress due to environmental, behavioral, and nutritional stressors and can lead to postweaning diarrhea and impaired gut development. The diet changes experienced during weaning require extensive adaptation of the digestive system. A well-developed piglet that had creep-feed experience before weaning performs better after weaning. In the current study, the effect of providing sow-fed piglets with a supplemental nutrient-dense complex milk replacer (NDM) on gut development and growth performance was studied. Litters of sows with similar parities (3.6 ± 0.8) and similar numbers of live born piglets (13.5 ± 0.3) were assigned to 1 of 2 groups: 1 group of piglets had ad libitum access to NDM from Day 2 through 21 after birth, whereas the other group was used as controls. Nutrient-dense complex milk replacer–fed piglets were shown to be significantly heavier after 21 d of supplementation compared with the control piglets. At Day 21, 3 piglets from each litter were euthanized for morphological and functional analyses of the intestinal tract. The small intestines of NDM-fed piglets had significantly higher weights (g) as well as significantly higher relative weight:length ratios (g//cm) compared with the small intestines of control piglets (P <0.05). Morphometric analysis demonstrated that villi length and numbers of goblet cells did not differ between groups. However, NDM-fed piglets had deeper crypts (P <0.001) and an increased expression of the cell-proliferation marker proliferating cell nuclear antigen in crypts (P <0.05), suggesting higher cell-proliferation rates. The gene encoding IGF- 1 showed a tendency to higher gene expression in the jejunum from NDM-fed piglets (P = 0.07) compared with the jejunum from control piglets, suggesting that IGF-1 might be involved in the regulation of cell proliferation and intestinal growth. Finally, as a result of dietary fiber in NDM, piglets showed significantly increased concentrations of metabolic fermentation products. This suggests differences in metabolic activity in the colon between treatment groups. In conclusion, providing sow-fed piglets with NDM before weaning stimulates intestinal proliferation, leading to increased circular growth. Nutrient-dense complex milk replacer supplementation might, therefore, help piglets through the transition period at weaning by increased BW and increased capacity for uptake of nutrients.

Leaf sodium accumulation facilitates salt stress adaptation and preserves photosystem functionality in salt stressed Ocimum basilicum
Mancarella, S. ; Orsini, F. ; Oosten, M.J. van; Sanoubar, R. ; Stanghellini, C. ; Kondo, S. ; Gianquinto, G. ; Maggio, A. - \ 2016
Environmental and Experimental Botany 130 (2016). - ISSN 0098-8472 - p. 162 - 173.
Basil - Cation accumulation - Gene expression - Induction curve - Photosynthetic efficiency - Salinity

In this study, plant growth, water relations, ABA levels, ion accumulation patterns and chlorophyll fluorescence were functionally linked to salt stress tolerance of two basil cultivars (Napoletano and Genovese) with different stress sensitivity levels. Plants were treated with salty water at 0, 100 and 200 mM of NaCl. Potential photosynthetic efficiency, non-photochemical quenching and upregulation of photodamage protection by D1 protein revealed higher salt tolerance in Genovese plants, which also resulted in improved water balance and photosynthesis preservation. Upon stress, these plants accumulated also lower ABA and were less affected than Napoletano by salinity in terms of biomass production. Genovese plants were able to upregulate the expression of genes for ROS scavenging and cation transport. These results along with the ability of GEN plants to accumulate larger amount of Na+ in the leaf tissue indicate that this cultivar was better suited to partially use Na+ as osmoticum.

Dietary-induced chronic hypothyroidism negatively affects rat follicular development and ovulation rate and is associated with oxidative stress
Meng, Li ; Rijntjes, E. ; Swarts, Hans ; Bunschoten, Annelies ; Stelt, Inge van der; Keijer, Jaap ; Teerds, Katja - \ 2016
Biology of Reproduction 94 (2016)4. - ISSN 0006-3363
Follicular development - Gene expression - Hypothyroidism - Ovary - Oxidative damage

The long-term effects of chronic hypothyroidism on ovarian follicular development in adulthood are not well known. Using a rat model of chronic diet-induced hypothyroidism initiated in the fetal period, we investigated the effects of prolonged reduced plasma thyroid hormone concentrations on the ovarian follicular reserve and ovulation rate in prepubertal (12-day-old) and adult (64-day-old and 120-day-old) rats. Besides, antioxidant gene expression, mitochondrial density and the occurrence of oxidative stress were analyzed. Our results show that continuous hypothyroidism results in lower preantral and antral follicle numbers in adulthood, accompanied by a higher percentage of atretic follicles, when compared to euthyroid age-matched controls. Not surprisingly, ovulation rate was lower in the hypothyroid rats. At the age of 120 days, the mRNA and protein content of superoxide dismutase 1 (SOD1) were significantly increased while catalase (CAT) mRNA and protein content was significantly decreased, suggesting a disturbed antioxidant defense capacity of ovarian cells in the hypothyroid animals. This was supported by a significant reduction in the expression of peroxiredoxin 3 (Prdx3), thioredoxin reductase 1 (Txnrd1), and uncoupling protein 2 (Ucp2) and a downward trend in glutathione peroxidase 3 (Gpx3) and glutathione S-transferase mu 2 (Gstm2) expression. These changes in gene expression were likely responsible for the increased immunostaining of the oxidative stress marker 4-hydroxynonenal. Together these results suggest that chronic hypothyroidism initiated in the fetal/neonatal period results in a decreased ovulation rate associated with a disturbance of the antioxidant defense system in the ovary.

Transcriptional Responses to the Auxin Hormone
Weijers, Dolf ; Wagner, Doris - \ 2016
Annual Review of Plant Biology 67 (2016). - ISSN 1543-5008 - p. 539 - 574.
ARF - Auxin - Chromatin - Development - Gene expression - Specificity

Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

Flusilazole induces spatio-temporal expression patterns of retinoic acid-, differentiation- and sterol biosynthesis-related genes in the rat Whole Embryo Culture
Dimopoulou, Myrto ; Verhoef, Aart ; Ravenzwaay, Bennard van; Rietjens, Ivonne M.C.M. ; Piersma, Aldert H. - \ 2016
Reproductive Toxicology 64 (2016). - ISSN 0890-6238 - p. 77 - 85.
Developmental toxicity - Flusilazole - Gene expression - in situ hybridization - Retinoic acid - Time-dependent - Whole embryo culture

Embryotoxic responses are critically dependent on the timing of exposure during embryo development. Here, we examined the time- dependent developmental effects in rat embryos exposed to flusilazole (FLU), and their link to retinoic acid (RA) mediated pathways. To this end, we assessed the effects of 4. h exposure of rat embryos in vitro to 300. μM FLU during four developmental time windows (0-4, 4-8, 24-28 and 44-48. h), evaluating morphological parameters, expression and localization of five genes directly or indirectly linked with the RA pathway. These were RA- (Cyp26a1 and Dhrs3), differentiation- (Gbx2 and Cdx1) and sterol biosynthesis- (Cyp51) related genes. Extended exposure for 48. h to 300. μM FLU resulted in morphological changes, typical for triazoles and RA, while the 4. h exposure times did not. Time dependent significant upregulation of the five selected genes was observed. These results corroborate that the embryotoxic responses to FLU are correlated with the regulation of the RA pathway. Thus, these gene expression markers can be considered early biomarkers of FLU-induced potential developmental toxicity later in the development.

Learning from co-expression networks : Possibilities and challenges
Serin, Elise A.R. ; Nijveen, Harm ; Hilhorst, Henk W.M. ; Ligterink, Wilco - \ 2016
Frontiers in Plant Science 7 (2016). - ISSN 1664-462X
Co-expression - Gene expression - Gene networks - Gene prioritization - Transcriptomics

Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.

Interindividual variation in gene expression responses and metabolite formation in acetaminophen-exposed primary human hepatocytes
Jetten, M.J.A. ; Blanco Garcia, Ainhoa ; Coonen, M.L.J. ; Claessen, Sandra ; Herwijnen, M.H.M. van; Lommen, Arjen ; Delft, J.H.M. van; Peijnenburg, A.A.C.M. ; Kleinjans, J.C.S. - \ 2016
Archives of Toxicology (2016). - ISSN 0340-5761 - p. 1103 - 1115.
Aflatoxin b1 - Benzo(a)pyrene - DNA methylation - Gene expression - Interindividual variation - Primary human hepatocytes

Acetaminophen (APAP) is a readily available over-the-counter drug and is one of the most commonly used analgesics/antipyretics worldwide. Large interindividual variation in susceptibility toward APAP-induced liver failure has been reported. However, the exact underlying factors causing this variability in susceptibility are still largely unknown. The aim of this study was to better understand this variability in response to APAP by evaluating interindividual differences in gene expression changes and APAP metabolite formation in primary human hepatocytes (PHH) from several donors (n = 5) exposed in vitro to a non-toxic to toxic APAP dose range. To evaluate interindividual variation, gene expression data/levels of metabolites were plotted against APAP dose/donor. The correlation in APAP dose response between donors was calculated by comparing data points from one donor to the data points of all other donors using a Pearson-based correlation analysis. From that, a correlation score/donor for each gene/metabolite was defined, representing the similarity of the omics response to APAP in PHH of a particular donor to all other donors. The top 1 % highest variable genes were selected for further evaluation using gene set overrepresentation analysis. The biological processes in which the genes with high interindividual variation in expression were involved include liver regeneration, inflammatory responses, mitochondrial stress responses, hepatocarcinogenesis, cell cycle, and drug efficacy. Additionally, the interindividual variation in the expression of these genes could be associated with the variability in expression levels of hydroxyl/methoxy-APAP and C8H13O5N-APAP-glucuronide. The before-mentioned metabolites or their derivatives have also been reported in blood of humans exposed to therapeutic APAP doses. Possibly these findings can contribute to elucidating the causative factors of interindividual susceptibility toward APAP.

Oviposition but not sex allocation is associated with transcriptomic changes in females of the parasitoid wasp Nasonia vitripennis
Cook, Nicola ; Trivedi, Urmi ; Pannebakker, B.A. ; Blaxter, Mark ; Ritchie, Michael G. ; Tauber, Eran ; Sneddon, Tanya ; Shuker, David M. - \ 2015
G3 : Genes Genomes Genetics 5 (2015)12. - ISSN 2160-1836 - p. 2885 - 2892.
Behavior - Competition - Gene expression - Local mate - Sex allocation - Transcriptomics

Linking the evolution of the phenotype to the underlying genotype is a key aim of evolutionary genetics and is crucial to our understanding of how natural selection shapes a trait. Here, we consider the genetic basis of sex allocation behavior in the parasitoid wasp Nasonia vitripennis using a transcriptomics approach. Females allocate offspring sex in line with the local mate competition (LMC) theory. Female-biased sex ratios are produced when one or a few females lay eggs on a patch. As the number of females contributing offspring to a patch increases, less female-biased sex ratios are favored. We contrasted the transcriptomic responses of females as they oviposit under conditions known to influence sex allocation: foundress number (a social cue) and the state of the host (parasitized or not). We found that when females encounter other females on a patch or assess host quality with their ovipositors, the resulting changes in sex allocation is not associated with significant changes in whole-body gene expression. We also found that the gene expression changes produced by females as they facultatively allocate sex in response to a host cue and a social cue are very closely correlated. We expanded the list of candidate genes associated with oviposition behavior in Nasonia, some of which may be involved in fundamental processes underlying the ability to facultatively allocate sex, including sperm storage and utilization.

SCB1, a BURP-domain protein gene, from developing soybean seed coats
Batchelor, A.K. ; Boutilier, K. ; Miller, S.S. ; Hattori, J. ; Bowman, L.U. ; Hu, M. ; Lantin, S. ; Johnson, D.A. ; Miki, B.L.A. - \ 2002
Planta 215 (2002). - ISSN 0032-0935 - p. 523 - 532.
Burp domain - Gene expression - Parenchyma cells - Seed coat - Tgm - Glycine
We describe a gene, SCB1 (Seed Coat BURP-domain protein 1), that is expressed specifically within the soybean (Glycine max [L.] Merrill) seed coat early in its development. Northern blot analysis and mRNA in situ hybridization revealed novel patterns of gene expression during seed development. SCB1 mRNA accumulated first within the developing thick-walled parenchyma cells of the inner integument and later in the thick- and thin-walled parenchyma cells of the outer integument. This occurred prior to the period of seed coat maturation and seed filling and before either of the layers started to degrade. SCB1 may therefore play a role in the differentiation of the seed coat parenchyma cells. In addition, the protein product appears to be located within cell walls. The SCB1 gene codes for a new member of a class of modular proteins that possess a carboxy-terminal BURP domain and a variety of different repeated sequences. The sequence of the genomic clone revealed the insertion of a Tgm transposable element in the upstream promoter region but it is not certain whether it contributes to the tissue-specific pattern of SCB1 expression.
Check title to add to marked list
<< previous | next >>

Show 20 50 100 records per page

 
Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.