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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Transcriptome and proteome analyses of proteases in biotroph fungal pathogen Cladosporium fulvum
Karimi Jashni, Mansoor ; Burgt, Ate van der; Battaglia, Evy ; Mehrabi, Rahim ; Collemare, Jérôme ; Wit, Pierre J.G.M. de - \ 2019
Journal of plant pathology - Formerly Rivista di patologia vegetale (2019). - ISSN 1125-4653 - 10 p.
Cladosoprium fulvum - Fungal proteases - Gene expression - Plant-microbe interaction - Tomato pathogen

Proteases are key components of the hydrolytic enzyme arsenal employed by fungal pathogens to invade their host plants. The recent advances in -omics era have facilitated identification of functional proteases involved in plant-fungus interactions. By comparison of the publically available sequences of fungal genomes we found that the number of protease genes present in the genome of Cladosporium fulvum, a biotrophic tomato pathogen, is comparable with that of hemibiotrophs. To identify host plant inducible protease genes and their products, we performed transcriptome and proteome analyses of C. fulvumin vitro and in planta by means of RNA-Seq/RT-qPCR and mass spectrometry. Transcriptome data showed that 14 out of the 59 predicted proteases are expressed during in vitro and in planta growth of C. fulvum, of which nine belong to serine proteases S8 and S10 and the rest belong to metallo- and aspartic proteases. Mass spectrometry confirmed the presence of six proteases at proteome level during plant infection. Expression of limited number of proteases by C. fulvum might sustain biotrophic growth and benefits its stealth pathogenesis.

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.
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.
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