Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    We will mail you new results for this query: keywords==Gene expression
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Shoot sodium exclusion in salt stressed barley (Hordeum vulgare L.) is determined by allele specific increased expression of HKT1;5
Bezouw, Roel F.H.M. van; Janssen, Elly M. ; Ashrafuzzaman, Md ; Ghahramanzadeh, Robab ; Kilian, Benjamin ; Graner, Andreas ; Visser, Richard G.F. ; Linden, Gerard van der - \ 2019
Journal of Plant Physiology 241 (2019). - ISSN 0176-1617
Barley - Gene expression - HKT1;5 - Naexclusion - Salt tolerance

High affinity potassium transporters (HKT) are recognized as important genes for crop salt tolerance improvement. In this study, we investigated HvHKT1;5 as a candidate gene for a previously discovered quantitative trait locus that controls shoot Na+ and Na+/K+ ratio in salt-stressed barley lines on a hydroponic system. Two major haplotype groups could be distinguished for this gene in a barley collection of 95 genotypes based on the presence of three intronic insertions; a designated haplotype group A (HGA, same as reference sequence) and haplotype group B (HGB, with insertions). HGB was associated with a much stronger root expression of HKT1;5 compared to HGA, and consequently higher K+ and lower Na+ and Cl concentrations and a lower Na+/K+ ratio in the shoots three weeks after exposure to 200 mM NaCl. Our experimental results suggest that allelic variation in the promoter region of the HGB gene is linked to the three insertions may be responsible for the observed increase in expression of HvHKT1;5 alleles after one week of salt stress induction. This study shows that in barley - similar to wheat and rice - HKT1;5 is an important contributor to natural variation in shoot Na+ exclusion.

Contribution of methylation regulation of MpDREB2A promoter to drought resistance of Mauls prunifolia
Li, Xuewei ; Xie, Yinpeng ; Lu, Liyuan ; Yan, Mingjia ; Fang, Nan ; Xu, Jidi ; Wang, Liping ; Yan, Yan ; Zhao, Tao ; Nocker, Steve van; Ma, Fengwang ; Liang, Dong ; Guan, Qingmei - \ 2019
Plant and Soil 441 (2019)1-2. - ISSN 0032-079X - p. 15 - 32.
ChIP-seq - DNA methylation - DREB2A - Drought resistance - Gene expression - Malus

Background and aims: Malus prunifolia (Chinese name: Fu Ping Qiu Zi), a wild relative of cultivated apple (Malus x domestica Borkh), is extremely resistant to drought compared with domesticated cultivars, such as ‘Golden Delicious’. However, the molecular mechanisms underlying drought resistance of M. prunifolia have not been characterized. This study investigates a new regulatory mechanism to improve apple drought resistance. Methods: M. prunifolia and ‘Golden Delicious’ were each grafted on M. hupehensis for gene expression analysis. The methylation level of the DREB2A promoter was determined by bisulfite sequencing and ChIP-qPCR. Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify target genes of MpDREB2A in apple. Results: The exposure to drought stress stimulated the expression level of DREB2A gene more than 100-fold in M. prunifolia, but only 16-fold in ‘Golden Delicious’. This difference in gene expression could not be explained in terms of difference in leaf relative water content. Correspondingly, the methylation level of M. prunifolia DREB2A (MpDREB2A) promoter region was significantly reduced. Additionally, MpDREB2A conferred enhanced drought resistance when ectopically expressed in Arabidopsis. Over 2800 potential downstream target genes of MpDREB2A were identified by ChIP-seq and these downstream genes have diverse potential functions related to stress resistance. Conclusions: Methylation regulation in promoter of MpDREB2A may contribute to the drought resistance of M. prunifolia.

Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets
Schokker, Dirkjan ; Hulsegge, Ina ; Woelders, Henri ; Rebel, Johanna M.J. - \ 2019
BMC Genomics 20 (2019)1. - ISSN 1471-2164
Development - Gene expression - Gut - Pig - Plasticity

Background: Immediately after birth, the porcine intestine rapidly develops morphologically, functionally, and immunologically. The jejunum, the second part of the small intestine, is of importance for nutrient uptake and immune surveillance. To study the early postnatal development of the jejunum, a meta-analysis was performed on different transcriptomic datasets. These datasets were acquired from different experimental in-house studies or from experiments described in literature of porcine jejunum mucosa. Gene expression was measured under different experimental interventions, such as nutritional intervention, at various time-points (age). Results: The studies included in the meta-analysis provided gene expression data for various time-points (piglet ages) for piglets that had received a treatment versus control piglets. In separate studies, treatments were administered to the sow (i.e. amoxicillin), or nutritional supplementation directly to the piglets with medium chain fatty acids (MCFAs), and oral administration of fructooligosaccharides (FOS) or a high dose of zinc-oxide, respectively. In the meta-analysis, genes were grouped into 16 clusters according to their temporal gene expression profiles for control piglets, i.e. the changes of gene expression level over time. Functional analysis showed that these temporal profile clusters had different dominant processes, such as immune related processes or barrier function. Transcriptomics data of treatment piglets was subsequently superimposed over the control temporal profiles. In this way we could investigate which temporal profile clusters (and which biological processes) were modulated by the treatments. Interestingly, not all 16 temporal profiles were modulated. Conclusions: We showed that it is possible to re-use (publicly available) transcriptomics data and produce temporal gene expression profiles for control piglets with overexpression of genes representing specific biological processes. Subsequently, by superimposing gene expression data from (nutritional) intervention studies we observed deviations from some of these reference profile(s) and thus the plasticity of the system. By employing this meta-analysis approach we highlighted the importance of birth and weaning and the underlying biological processes.

Morphological and quality characterization of grape berry and rachis in response to postharvest 1-methylcyclopropene and elevated oxygen and carbon dioxide atmospheres
Wang, Lei ; Luo, Zisheng ; Li, Junhao ; Yang, Mingyi ; Yan, Jiawei ; Lu, Hongyan ; Li, Dong ; Chen, Cunkun ; Aghdam, Morteza Soleimani ; Wu, Bin ; Li, Li - \ 2019
Postharvest Biology and Technology 153 (2019). - ISSN 0925-5214 - p. 107 - 117.
1-Methylcyclopropene - Berry - Elevated O /CO atmosphere - Gene expression - Rachis

This research studied the morphological characterization and quality attributes of ‘Kyoho’ and ‘Yongyou NO.1’ (Vitis vinifera L. × Vitis labrusca L.) grape berry and rachis in response to postharvest treatment with 1-methylcyclopropene (1-MCP) alone or in combination with elevated 80% O 2 (H-O 2 ) / 20% CO 2 (H-CO 2 ). Results indicated that the integrated application of exogenous 1-MCP alone and combined with H-O 2 /H-CO 2 significantly prevented the rachis browning and chlorophyll degradation, maintained the cellular microstructure integrity and promoted esters and terpenes synthesis. Additionally, the transcriptional expression of genes involved in ethylene biosynthesis was sharply downregulated by 1-MCP treatment in both cultivar rachis and berries. And genes expression related to softening was also downregulated by 1-MCP alone and plus elevated O 2 /CO 2 atmospheres treatment. Particularly, the combinatorial treatment of 1-MCP and H-O 2 effectively impeded berry abscission and alcohols accumulation; whereas 1-MCP with H-CO 2 treatment maintained the membrane permeability in berries. Nevertheless, 1-MCP alone or in combination with elevated atmospheres did not significantly affect total soluble solids and titratable acidity and did not harm sensory quality in both ‘Kyoho’ and ‘Yongyou NO.1’ cultivars after 32 days of storage.

Transcriptional response of cultured porcine intestinal epithelial cells to micro algae extracts in the presence and absence of enterotoxigenic Escherichia coli
Hulst, Marcel ; Weide, Rommie Van der; Hoekman, Arjan ; Krimpen, Marinus Van - \ 2019
Genes & Nutrition 14 (2019)1. - ISSN 1555-8932
Enterotoxigenic Escherichia coli - Food/feed additive - Gene expression - Intestinal cells - Micro algae

Background: Micro algae’s are worldwide considered as an alternative source of proteins in diets for animals and humans. Micro algae also produce an array of biological active substances with potential to induce beneficial and health promoting effects. To better understand the mode of action of micro algae’s when applied as additive in diets, porcine intestinal epithelial cells (IPEC-J2), stressed by enterotoxigenic Escherichia coli (ETEC) or under non-stressed conditions, were exposed to micro algae extracts and changes in gene expression were recorded. Methods: IPEC-J2 cells were exposed for 2 and 6 h to extracts prepared from the biomass of the microalgae Chlorella vulgaris (C), Haematococcus pluvialis (H), Spirulina platensis (S), or a mixture of Scenedesmus obliques and Chlorella sorokiniana (AM), in the absence and presence of ETEC. Gene expression in cells was measured using porcine “whole genome” microarrays. Results: The micro algae extracts alone enhanced the expression of a set of genes coding for proteins with biological activity that are secreted from cells. These secreted proteins (hereafter denoted as effector proteins; EPs) may regulate processes like remodelling of the extracellular matrix, activation of an antiviral/bacterial response and oxygen homeostasis in the intestine and periphery. Elevated gene expression of immunostimulatory proteins CCL17, CXCL2, CXCL8 (alias IL8), IFNA, IFNL1, HMOX1, ITGB3, and THBS1 was observed in response to all four extracts in the absence or presence of ETEC. For several of these immunostimulatory proteins no elevated expression was observed when cells were exposed to ETEC alone. Furthermore, all extracts highly stimulated expression of an antisense RNA of the mitochondrial/peroxisome symporter SLC25A21 gene in ETEC-challenged cells. Inhibition of SLC25A21 translation by this antisense RNA may impose a concentration gradient of 2-oxoadipic and 2-oxoglutarate, both metabolites of fatty acid β-oxidation, between the cytoplasm and the interior of these organelles. Conclusions: Exposure of by ETEC stressed intestinal epithelium cells to micro algae extracts affected “fatty acid β-oxidation”, ATP and reactive oxygen species production and (de) hydroxylation of lysine residues in procollagen chains in these cells. Elevated gene expression of specific EPs and immunostimulatory proteins indicated that micro algae extracts, when used as feed/food additive, can steer an array of metabolic and immunological processes in the intestines of humans and monogastric animals stressed by an enteric bacterial pathogen.

Discovering novel hydrolases from hot environments
Wohlgemuth, Roland ; Littlechild, Jennifer ; Monti, Daniela ; Schnorr, Kirk ; Rossum, Teunke van; Siebers, Bettina ; Menzel, Peter ; Kublanov, Ilya V. ; Rike, Anne Gunn ; Skretas, Georgios ; Szabo, Zalan ; Peng, Xu ; Young, Mark J. - \ 2018
Biotechnology Advances 36 (2018)8. - ISSN 0734-9750 - p. 2077 - 2100.
Biocatalysis - Enrichment - Enzyme characterization - Enzyme screening - Gene expression - Genomics - Hydrolases - Metagenomics - Sequencing - Thermophiles

Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.

Soy supplementation : Impact on gene expression in different tissues of ovariectomized rats and evaluation of the rat model to predict (post)menopausal health effect
Islam, Mohammed A. ; Hooiveld, Guido J.E.J. ; Berg, Johannes H.J. van den; Velpen, Vera van der; Murk, Albertinka J. ; Rietjens, Ivonne M.C.M. ; Leeuwen, F.X.R. van - \ 2018
Toxicology Reports 5 (2018). - ISSN 2214-7500 - p. 1087 - 1097.
(Post)menopausal health effect - Gene expression - Ovariectomized rat model - Soy isoflavone supplementation

This toxicogenomic study was conducted to predict (post)menopausal human health effects of commercial soy supplementation using ovariectomized rats as a model. Different target tissues (i.e. breast, uterus and sternum) and non-target tissues (i.e. peripheral blood mononuclear cells (PBMC), adipose and liver) of ovariectomized F344 rats exposed to a commercially available soy supplement for eight weeks, were investigated. Changes in gene expression in these tissues were analysed using whole-genome microarray analysis. No correlation in changes in gene expression were observed among different tissues, indicating tissue specific effects of soy isoflavone supplementation. Out of 87 well-established estrogen responsive genes (ERGs), only 19 were found to be significantly regulated (p < 0.05) in different tissues, particularly in liver, adipose and uterus tissues. Surprisingly, no ERGs were significantly regulated in estrogen sensitive breast and sternum tissues. The changes in gene expression in PBMC and adipose tissue in rats were compared with those in (post)menopausal female volunteers who received the same supplement in a similar oral dose and exposure duration in human intervention studies. No correlation in changes in gene expression between rats and humans was observed. Although receiving a similar dose, in humans the plasma levels expressed as total free aglycones were several folds higher than in the rat. Therefore, the overall results in young ovariectomized female F344 rats indicated that using rat transcriptomic data does not provide a suitable model for human risk or benefit analysis of soy isoflavone supplementation.

The influence of microplastics and halogenated contaminants in feed on toxicokinetics and gene expression in European seabass (Dicentrarchus labrax)
Granby, Kit ; Rainieri, Sandra ; Rasmussen, Rie Romme ; Kotterman, Michiel J.J. ; Sloth, Jens Jørgen ; Cederberg, Tommy Licht ; Barranco, Alex ; Marques, António ; Larsen, Bodil Katrine - \ 2018
Environmental Research 164 (2018). - ISSN 0013-9351 - p. 430 - 443.
Elimination - Gene expression - Microplastics - PBDE - PCB
When microplastics pollute fish habitats, it may be ingested by fish, thereby contaminating fish with sorbed contaminants. The present study investigates how combinations of halogenated contaminants and microplastics associated with feed are able to alter toxicokinetics in European seabass and affect the fish. Microplastic particles (2%) were added to the feed either with sorbed contaminants or as a mixture of clean microplastics and chemical contaminants, and compared to feed containing contaminants without microplastics. For the contaminated microplastic diet, the accumulation of polychlorinated biphenyls (PCBs) and brominated flame retardants (BFRs) in fish was significantly higher, increasing up to 40 days of accumulation and then reversing to values comparable to the other diets at the end of accumulation. The significant gene expression results of liver (cyp1a, il1β gstα) after 40 days of exposure indicate that microplastics might indeed exacerbate the toxic effects (liver metabolism, immune system, oxidative stress) of some chemical contaminants sorbed to microplastics. Seabass quickly metabolised BDE99 to BDE47 by debromination, probably mediated by deiodinase enzymes, and unlike other contaminants, this metabolism was unaffected by the presence of microplastics. For the other PCBs and BFRs, the elimination coefficients were significantly lower in fish fed the diet with contaminants sorbed to microplastic compared to the other diets. The results indicate that microplastics affects liver detoxification and lipid distribution, both of which affect the concentration of contaminants.
Lifelong calorie restriction affects indicators of colonic health in aging C57Bl/6J mice
Kok, Dieuwertje E.G. ; Rusli, Fenni ; Lugt, Benthe van der; Lute, Carolien ; Laghi, Luca ; Salvioli, Stefano ; Picone, Gianfranco ; Franceschi, Claudio ; Smidt, Hauke ; Vervoort, Jacques ; Kampman, Ellen ; Müller, Michael ; Steegenga, Wilma T. - \ 2018
Journal of Nutritional Biochemistry 56 (2018). - ISSN 0955-2863 - p. 152 - 164.
Aging - Calorie restriction - Colonic health - Gene expression - Gut microbiota - Metabolites
Diminished colonic health is associated with various age-related pathologies. Calorie restriction (CR) is an effective strategy to increase healthy lifespan, although underlying mechanisms are not fully elucidated. Here, we report the effects of lifelong CR on indicators of colonic health in aging C57Bl/6J mice. Compared to an ad libitum control and moderate-fat diet, 30% energy reduction was associated with attenuated immune- and inflammation-related gene expression in the colon. Furthermore, expression of genes involved in lipid metabolism was higher upon CR, which may point towards efficient regulation of energy metabolism. The relative abundance of bacteria considered beneficial to colonic health, such as Bifidobacterium and Lactobacillus, increased in the mice exposed to CR for 28 months as compared to the other diet groups. We found lower plasma levels of interleukin-6 and lower levels of various metabolites, among which are bile acids, in the colonic luminal content of CR-exposed mice as compared to the other diet groups. Switching from CR to an ad libitum moderate-fat diet at old age (24 months) revealed remarkable phenotypic plasticity in terms of gene expression, microbiota composition and metabolite levels, although expression of a subset of genes remained CR-associated. This study demonstrated in a comprehensive way that CR affects indicators of colonic health in aging mice. Our findings provide unique leads for further studies that need to address optimal and feasible strategies for prolonged energy deprivation, which may contribute to healthy aging.
Select skeletal muscle mRNAs related to exercise adaptation are minimally affected by different pre-exercise meals that differ in macronutrient profile
Knuiman, Pim ; Hopman, Maria T.E. ; Wouters, Jeroen A. ; Mensink, Marco - \ 2018
Frontiers in Physiology 9 (2018)JAN. - ISSN 1664-042X
Endurance exercise - Gene expression - Humans - Nutrient availability - Resistance exercise
Background: Substantial research has been done on the impact of carbohydrate and fat availability on endurance exercise adaptation, though its role in the acute adaptive response to resistance exercise has yet to be fully characterized. Purpose: We aimed to assess the effects of a pre-resistance exercise isocaloric mixed meal containing different amounts of carbohydrates and fat, on post-resistance exercise gene expression associated with muscle adaptation. Methods: Thirteen young (age 21.2 ± 1.6 year), recreationally trained (VO2max 51.3 ± 4.8 ml/kg/min) men undertook an aerobic exercise session of 90-min continuous cycling (70% VO2max) in the morning with pre- and post-exercise protein ingestion (10 and 15 g casein in a 500 ml beverage pre- and post-exercise, respectively). Subjects then rested for 2 h and were provided with a meal consisting of either 3207 kJ; 52 g protein; 51 g fat; and 23 g carbohydrate (FAT) or 3124 kJ; 53 g protein; 9 g fat; and 109 g carbohydrate (CHO). Two hours after the meal, subjects completed 5 × 8 repetitions (80% 1-RM) for both bilateral leg press and leg extension directly followed by 25 g of whey protein (500 ml beverage). Muscle biopsies were obtained from the vastus lateralis at baseline (morning) and 1 and 3 h post-resistance exercise (afternoon) to determine intramuscular mRNA response. Results: Muscle glycogen levels were significantly decreased post-resistance exercise, without any differences between conditions. Plasma free fatty acids increased significantly after the mixed meal in the FAT condition, while glucose and insulin were higher in the CHO condition. However, PDK4 mRNA quantity was significantly higher in the FAT condition at 3 h post-resistance exercise compared to CHO. HBEGF, INSIG1, MAFbx, MURF1, SIRT1, and myostatin responded solely as a result of exercise without any differences between the CHO and FAT group. FOXO3A, IGF-1, PGC-1a, and VCP expression levels remained unchanged over the course of the day. Conclusion: We conclude that mRNA quantity associated with muscle adaptation after resistance exercise is not affected by a difference in pre-exercise nutrient availability. PDK4 was differentially expressed between CHO and FAT groups, suggesting a potential shift toward fat oxidation and reduced glucose oxidation in the FAT group.
Triclosan-induced transcriptional and biochemical alterations in the freshwater green algae Chlamydomonas reinhardtii
Pan, Chang Gui ; Peng, Feng-Jiao ; Shi, Wen Jun ; Hu, Li Xin ; Wei, Xiao Dong ; Ying, Guang Guo - \ 2018
Ecotoxicology and Environmental Safety 148 (2018). - ISSN 0147-6513 - p. 393 - 401.
Biochemical alteration - Chlamydomonas reinhardtii - Gene expression - Growth - Toxicity - Triclosan

Triclosan (TCS) is an antibacterial and antifungal agent widely used in personal care products (PCPs). We investigated the effects of TCS (20 μg/L, 100 μg/L and 500 μg/L) on Chlamydomonas reinhardtii by measuring the algal growth, chlorophyll content, lipid peroxidation, and transcription of the antioxidant-related genes (superoxide dismutase (SOD), glutathione peroxidase (GPX), catalase (CAT), glutathione S-transferase (GST), plastid terminal oxidase 2 (PTOX) and thioredoxin (TRX)) as well as biochemical alterations. The results showed significant dose-related effects of TCS on the algal species in terms of growth and chlorophyll content. Malondialdehyde (MDA) increased with increasing TCS concentrations and showed significant difference between the treatment of 405.3 μg/L TCS and control group. Transcription analysis revealed that the expression of SOD mRNA was most sensitive to TCS among the selected genes. In addition, Fourier-transform infrared spectroscopy showed time- and concentration-specific biochemical responses in C. reinhardtii when exposed to TCS. The biochemical alterations associated with different doses of TCS were mainly attributed to structural changes associated with lipid, protein, nucleic acid and carbohydrate. The findings from this study reveal that TCS in the aquatic environment may affect algal growth, chlorophyll synthesis, oxidative stress responses and cause biochemical alterations. This study provided important information to achieve a better understanding of the toxic mechanism of triclosan on algae Chlamydomonas reinhardtii.

Brassica rapa hairy root extracts promote skin depigmentation by modulating melanin production and distribution
Sena, Luigi Michele ; Zappelli, Claudia ; Apone, Fabio ; Barbulova, Ani ; Tito, Annalisa ; Leone, Antonella ; Oliviero, Teresa ; Ferracane, Rosalia ; Fogliano, Vincenzo ; Colucci, Gabriella - \ 2018
Journal of Cosmetic Dermatology 17 (2018)2. - ISSN 1473-2130 - p. 246 - 257.
Active ingredient - Cell biology - Depigmentation - Gene expression - Hairy root cultures - Melanogenesis

Background: Skin whitening products, used for ages by Asian people for cultural and esthetic purposes, are very popular nowadays in Western countries as well, where the need to inhibit skin spots after sun exposure has become not only a cosmetic but also a health-related issue. Thus, the development of effective and safe depigmenting agents derived from natural products gets continuous attention by cosmetic brands and consumers. Objectives: The aim of this study was to determine the effects of two preparations, obtained from the hairy root cultures of the species Brassica rapa, on melanogenesis and the expression of the extracellular matrix proteins involved in a correct pigment distribution. Methods: The two preparations, obtained by water-ethanol extraction and by digestion of cell-wall glycoproteins of the root cells, were chemically characterized and tested on skin cell cultures and on human skin explants to investigate on their dermatological activities. Results: Both the extracts were able to decrease melanin synthesis pathway in melanocytes and modulate the expression of genes involved in melanin distribution. One of the extracts was also effective in inducing the expression of laminin-5 and collagen IV, involved into the maintenance of tissue integrity. The two extracts, when tested together on human skin explants, demonstrated a good synergic hypopigmenting activity. Conclusions: Taken together, the results indicate that the extracts from B. rapa root cultures can be employed as cosmetic active ingredients in skin whitening products and as potential therapeutic agents for treating pigmentation disorders.

Infection of a tomato cell culture by Phytophthora infestans; a versatile tool to study Phytophthora-host interactions
Schoina, Charikleia ; Bouwmeester, Klaas ; Govers, Francine - \ 2017
Plant Methods 13 (2017). - ISSN 1746-4811 - 14 p.
Cell death - Defense responses - Disease - Gene expression - Infection - Microscopy - MsK8 - Reactive oxygen species (ROS)

Background: The oomycete Phytophthora infestans causes late blight on potato and tomato. Despite extensive research, the P. infestans-host interaction is still poorly understood. To find new ways to further unravel this interaction we established a new infection system using MsK8 tomato cells. These cells grow in suspension and can be maintained as a stable cell line that is representative for tomato. Results: MsK8 cells can host several Phytophthora species pathogenic on tomato. Species not pathogenic on tomato could not infect. Microscopy revealed that 16 h after inoculation up to 36% of the cells were infected. The majority were penetrated by a germ tube emerging from a cyst (i.e. primary infection) while other cells were already showing secondary infections including haustoria. In incompatible interactions, MsK8 cells showed defense responses, namely reactive oxygen species production and cell death leading to a halt in pathogen spread at the single cell level. In compatible interactions, several P. infestans genes, including RXLR effector genes, were expressed and in both, compatible and incompatible interactions tomato genes involved in defense were differentially expressed. Conclusions: Our results show that P. infestans can prosper as a pathogen in MsK8 cells; it not only infects, but also makes haustoria and sporulates, and it receives signals that activate gene expression. Moreover, MsK8 cells have the ability to support pathogen growth but also to defend themselves against infection in a similar way as whole plants. An advantage of MsK8 cells compared to leaves is the more synchronized infection, as all cells have an equal chance of being infected. Moreover, analyses and sampling of infected tissue can be performed in a non-destructive manner from early time points of infection onwards and as such the MsK8 infection system offers a potential platform for large-scale omics studies and activity screenings of inhibitory compounds.

A validated, transitional and translational porcine model of hepatocellular carcinoma
Schachtschneider, Kyle M. ; Schwind, Regina M. ; Darfour-Oduro, Kwame A. ; De, Arun K. ; Rund, Lauretta A. ; Singh, Kuldeep ; Principe, Daniel R. ; Guzman, Grace ; Ray, Charles E. ; Ozer, Howard ; Gaba, Ron C. ; Schook, Lawrence B. - \ 2017
Oncotarget 8 (2017)38. - ISSN 1949-2553 - p. 63620 - 63634.
Gene expression - Hepatocellular carcinoma - Human - Interventional radiology - Porcine model

Difficult questions are confronting clinicians attempting to improve hepatocellular carcinoma (HCC) outcomes. A large animal model with genetic, anatomical, and physiological similarities to humans is required to transition from mouse models to human clinical trials to address unmet clinical needs. To validate our previously reported inducible porcine cancer model (Oncopig) as a transitional HCC model, Oncopig hepatocyte cultures were transformed using Cre recombinase. The resulting porcine HCC cells (pHCC) expressed oncogenic TP53R167H and KRASG12D, and displayed nuclear pleomorphisms with pale to granular cytoplasm arranged in expanded plates similar to human HCC histopathology. Human HCC transcriptional hallmarks were detected in pHCC cells using RNA-seq, including TERT reactivation, apoptosis evasion, angiogenesis activation, and Wnt signaling activation. Master regulators of gene expression were conserved across Oncopig and 18 human HCC cell lines. pHCC injection into SCID mice resulted in tumors recapitulating human HCC characteristics, including thick trabeculae formation, pseudoacini patterning, and sheets of wellvascularized stroma. Finally, autologous injection of pHCC cells subcutaneously yielded a tumor histologically characterized as Edmondson Steiner (HCC nuclear grade assessment system) grade 2 HCC with trabecular patterning and T-lymphocyte infiltration. These data demonstrate the Oncopig HCC model's utility for improving detection, treatment, and biomarker discovery relevant to human HCC.

Functional characterization of cucumber (Cucumis sativus L.) Clade V MLO genes
Berg, Jeroen A. ; Appiano, Michela ; Bijsterbosch, Gerard ; Visser, Richard G.F. ; Schouten, Henk J. ; Bai, Yuling - \ 2017
BMC Plant Biology 17 (2017)1. - ISSN 1471-2229
Cucumber (Cucumis sativus L.) - Gene expression - MLO - Powdery mildew - Susceptibility genes

Background: Powdery mildew (PM) causing fungi are well-known pathogens, infecting over 10.000 plant species, including the economically important crop cucumber (Cucumis sativus L.). Loss-of-function mutations in clade V MLO genes have previously been shown to lead to recessively inherited broad-spectrum resistance to PM in several species. In cucumber, one clade V MLO homolog (CsaMLO8) was previously identified as being a susceptibility factor to PM. Two other closely related homologs (CsaMLO1 and CsaMLO11) were found, but their function was not yet unravelled. Methods: CsaMLO1 and CsaMLO11 were cloned from cucumber and overexpressed in a tomato mlo mutant. The transcript abundances of all three CsaMLO genes in different cucumber tissues were quantified using qRT-PCR and RNA-seq, with and without inoculation with the cucumber PM fungus Podosphaera xanthii. Allelic variation of CsaMLO1 and CsaMLO11 was screened in silico in sequenced cucumber germplasm. Results: Heterologous overexpression of all three CsaMLO genes in the tomato mlo mutant restored susceptibility to PM caused by Oidium neolycopersici, albeit to a different extent: whereas overexpression of CsaMLO1 or CsaMLO8 completely restored susceptibility, overexpression of CsaMLO11 was only partially able to restore PM susceptibility. Furthermore, it was observed by qRT-PCR and RNA-seq that CsaMLO8 was significantly higher expressed in non-inoculated cucumber compared to the other two MLO genes. However, inoculation with P. xanthii led to upregulation of CsaMLO1, but not to upregulation of CsaMLO8 or CsaMLO11. Conclusions: Both CsaMLO1 and CsaMLO11 are functional susceptibility genes, although we conclude that based on the transcript abundance CsaMLO8 is probably the major clade V MLO gene in cucumber regarding providing susceptibility to PM. Potential loss-of-function mutations in CsaMLO1 and CsaMLO11 have not been identified. The generation and analysis of such mutants are interesting subjects for further investigation.

A short-term intervention with selenium affects expression of genes implicated in the epithelial-to-mesenchymal transition in the prostate
Gils-Kok, Dieuwertje van; Kiemeney, Lambertus A.L.M. ; Verhaegh, Gerald W. ; Schalken, Jack A. ; Lin, Emile N.J.T. van; Sedelaar, J.P.M. ; Witjes, J.A. ; Hulsbergen-van de Kaa, Christina A. ; Veer, Pieter van 't; Kampman, Ellen ; Afman, Lydia A. - \ 2017
Oncotarget 8 (2017)6. - ISSN 1949-2553 - p. 10565 - 10579.
EMT - Gene expression - Microarray - Prostatic neoplasms - Selenium

In parallel with the inconsistency in observational studies and chemoprevention trials, the mechanisms by which selenium affects prostate cancer risk have not been elucidated. We conducted a randomized, placebo-controlled trial to examine the effects of a short-term intervention with selenium on gene expression in non-malignant prostate tissue. Twenty-three men received 300 μg selenium per day in the form of selenized yeast (n=12) or a placebo (n=11) during 5 weeks. Prostate biopsies collected from the transition zone before and after intervention were analysed for 15 participants (n=8 selenium, n=7 placebo). Pathway analyses revealed that the intervention with selenium was associated with down-regulated expression of genes involved in cellular migration, invasion, remodeling and immune responses. Specifically, expression of well-established epithelial markers, such as E-cadherin and epithelial cell adhesion molecule EPCAM, was up-regulated, while the mesenchymal markers vimentin and fibronectin were down-regulated after intervention with selenium. This implies an inhibitory effect of selenium on the epithelial-to-mesenchymal transition (EMT). Moreover, selenium was associated with down-regulated expression of genes involved in wound healing and inflammation; processes which are both related to EMT. In conclusion, our explorative data showed that selenium affected expression of genes implicated in EMT in the transition zone of the prostate.

Persistent organic pollutants alter DNA methylation during human adipocyte differentiation
Dungen, Myrthe W. van den; Murk, Albertinka J. ; Gils-Kok, Dieuwertje van; Steegenga, Wilma T. - \ 2017
Toxicology in Vitro 40 (2017). - ISSN 0887-2333 - p. 79 - 87.
Adipocytes - DNA methylation - Gene expression - Human mesenchymal stem cells - Infinium 450K BeadChip - Persistent organic pollutants (POPs)

Ubiquitous persistent organic pollutants (POPs) can accumulate in humans where they might influence differentiation of adipocytes. The aim of this study was to investigate whether DNA methylation is one of the underlying mechanisms by which POPs affect adipocyte differentiation, and to what extent DNA methylation can be related to gene transcription. Adipocyte differentiation was induced in two human cell models with continuous exposure to different POPs throughout differentiation. From the seven tested POPs, perfluorooctanesulfonic acid (PFOS) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) decreased lipid accumulation, while tributyltin (TBT) increased lipid accumulation. In human mesenchymal stem cells (hMSCs), TCDD and TBT induced opposite gene expression profiles, whereas after PFOS exposure gene expression remained relatively stable. Genome-wide DNA methylation analysis showed that all three POPs affected DNA methylation patterns in adipogenic and other genes, possibly related to the phenotypic outcome, but without concomitant gene expression changes. Differential methylation was predominantly detected in intergenic regions, where the biological relevance of alterations in DNA methylation is unclear. This study demonstrates that POPs, at environmentally relevant levels, are able to induce differential DNA methylation in human differentiating adipocytes.

Effects and detection of Nandrosol and ractopamine administration in veal calves
Divari, Sara ; Berio, Enrica ; Pregel, Paola ; Sereno, Alessandra ; Chiesa, Luca ; Pavlovic, Radmila ; Panseri, Sara ; Bovee, Toine F.H. ; Biolatti, Bartolomeo ; Cannizzo, Francesca T. - \ 2017
Food Chemistry 221 (2017). - ISSN 0308-8146 - p. 706 - 713.
Bioassay - Gene expression - Histopathology - LC-MS/MS - Nandrosol - Ractopamine - SARM - Veal calves

The present study describes different effects of the selective androgen receptor modulator (SARM) nandrolone phenylpropionate (Nandrosol) and the β-agonist ractopamine administration in veal calves, and it investigates different strategies applied to trace these molecules. Morphological changes of gonads and accessory glands attributed to androgen effects, such as testicular atrophy, seminiferous tubule diameter reduction and hyperplasia of prostate epithelium, were detected, although SARMs are not described to cause these lesions. The gene expression analysis showed an anabolic activity of Nandrosol in Longissimus dorsi muscle, where myosin heavy chain (MYH) was significantly up-regulated. An IGF1 increase was weakly significant only in Vastus lateralis muscle. In conclusion, the anatomo-histopathological observations and the MYH mRNA up-regulation in Longissimus dorsi muscle confirm the androgenic treatment in experimental animals. The biosensor assay was not enough sensitive to detect residues in urines and only the direct chemical analysis of urine samples confirmed both β-agonist and SARM treatment.

Effect of Endoscopic Gastroplication on the Genome-Wide Transcriptome in the Upper Gastrointestinal Tract
Wielen, Nikkie van der; Paulus, Givan ; Avesaat, Mark van; Masclee, Ad ; Meijerink, Jocelijn ; Bouvy, Nicole - \ 2017
Obesity Surgery 27 (2017)3. - ISSN 0960-8923 - p. 740 - 748.
Adiponectin - Duodenum - Gastric tissue - Gastroplication - Gene expression - HbA1c - Immunity - Inflammation - Transcriptome
Background: Bariatric surgery is an effective intervention strategy in obesity, resulting in sustained weight loss and a reduction of comorbidities. Gastroplication, using the articulating circular endoscopic stapler, was recently introduced as a transoral bariatric technique. This procedure reduces gastric volume and induced 34.9 % of excess weight loss in the first year (Paulus et al. Gastrointest Endosc. 81(2):312–20, 3). The aim of the present study was to gain insight in the long-term effects and underlying mechanisms of gastroplication by investigating differences in the genome-wide gastric and duodenal transcriptome before and 1 year after intervention. Methods: Ten morbidly obese patients (BMI 39.8 ± 0.9 kg/m2 (mean ± SEM)) underwent gastroplication. Previous to the procedure and after 1 year, blood samples were taken, and mucosal biopsies were collected from the fundus, antrum and duodenum. Gene expression was measured using microarray analysis. Plasma adiponectin, HbA1c, IL-1β, IL-6, IL-7, TNF-α, IFN-γ, MCP-1, IL-8, TGF-1 and CRP levels were determined. Results: Downregulation of inflammatory genes and gene sets was observed in the fundus and duodenum 1 year after surgery. Gene expression of ghrelin and its activating enzyme GOAT were downregulated in the upper gastrointestinal tract. Patients showed a reduction in plasma HbA1c levels (from 6.17 ± 0.51 to 5.32 ± 0.14 %, p = 0.004) and an increase of plasma adiponectin (from 16.87 ± 3.67 to 27.67 ± 5.92 μg/ml, p = 0.002). Conclusions: Individuals undergoing gastroplication displayed a downregulation of inflammatory tone in the stomach and duodenum, which coincided with improved HbA1c and adiponectin levels. The reduction of inflammatory tone in the upper gastrointestinal tract may be a consequence of an improved metabolic health status or alternatively caused by the procedure itself.
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.
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