Expression data of Arabidopsis pollen tube of an AGP6 AGP11 double null mutant
Ontology highlight
ABSTRACT: Arabinogalactan proteins are proteoglycans known to have important roles during cell growth and development, namelly during pollen tube growth. A microarray experiment was performed on agp6 agp11 pollen tubes to search for genetic interactions in the context of pollen tube growth. RNA from wt and mutant pollen tubes was extracted after 8h of in vitro germination and hybridized on Affimetrix microarrays.
Project description:Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 20 and 110 mg/L of PYR (corresponding to the PYR IC20 and IC50, respectively), or in medium non-supplemented with the fungicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with both concentrations of PYR and with control cells were carried out together. For each exposure condition, independent biological triplicates were processed and analysed.
Project description:Despite their different origin and function, both pollen tubes and root hairs share the same sort of apical growth mechanism, i.e., the spatially focused cell expansion at the very apex. Ion fluxes, membrane trafficking, the actin cytoskeleton and their interconnection via signaling networks have been identified as fundamental processes underlying this kind of growth. Several molecules involved in apical growth have been identified, but the genetic basis is far from being fully characterized. We have used Affymetrix Arabidopsis ATH1 GeneChips to obtain the expression profiles of isolated Arabidopsis root hairs. A comparison with the expression profile of flow-sorted pollen grains reveals an overlap in the expression of 4989 genes, which corresponds to 42% of the root hair transcriptome and 76% of the pollen transcriptome, respectively. Our comparison with transcriptional profiles of vegetative tissues by principal component analysis and hierarchical clustering shows a clear separation of these samples comprised of cell types with diffuse growth from the two cell types with apical growth. 277 genes are enriched and 49 selectively expressed, respectively, in root hairs and pollen. From this set of genes emerges an apical growth signature containing novel candidate genes for apical growth determination. Root hairs were isolated from Arabidopsis seedlings and total RNA was isolated for expression profiling on Affymetrix ATH1 arrays. The study was performed with biological duplicates.
Project description:The world-wide used herbicide alachlor is among the priority substances listed in the European Water Framework Directive. We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to alachlor at concentrations exerting slight to moderate levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the lowest observed effect concentration (LOEC; ~8% growth inhibition) and the 20%-inhibitory concentration (IC20), compared to control cells not exposed to the herbicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 110 or 200 mg/L of ALA (corresponding to the LOEC and the IC20, respectively, of alachlor) or in medium non-supplemented with the herbicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with each concentration of alachlor versus controls were carried out independently. For each exposure condition, independent biological triplicates were processed and analysed.
Project description:The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to the well-established role of miRNAs as regulators of plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1 activation. To test this we have performed comparative analyses of the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis. To assess the impact of miRNA deficiency on the starvation response we performed transcriptomics analyses of WT and dcl1-9 plants by subjecting leaves to 6h of light (control) or darkness (starvation)
Project description:Nanoemulsion adjuvant affects immune gene expression in dendritic cells. Microarray was used to asses global changes in gene expression in JAWS II dendritic cells upon treatment with nanoemulsion (NE) adjuvant W805EC JawsII cell were incubated with NE formulation for 6 and 24 hours, and RNA was extracted for Affymetrix hybridization
Project description:COUP-TFII, a member of the nuclear receptor superfamily plays a critical role in angiogenesis and organogenesis during embryonic development. Our results indicate that COUP-TFII expression is profoundly upregulated in prostate cancer patients and might serves as biomarker for recurrence prediction. Thus we conduct transcriptome comparison of control and COUP-TFII depleted PC3 cells to gain genomic insights on the biological processes that COUP-TFII is involved in prostate cancer cells. Ingenuity Pathway Analysis (IPA) shows that the most prominent altered pathways in the COUP-TFII depleted cells are related to cell growth; cell cycle progression and DNA damage response. Indeed many growth related genes including E2F1, p21, CDC25A, Cyclin A and Cyclin B are changed in COUP-TFII knockdown cells, suggesting that COUP-TFII might be an important regulator for prostate cancer cell growth. Further functional assays from cells and mice genetic studies confirm the hypothesis that COUP-TFII serve as the major regulator to control prostrate cancer growth. Together, results provide insight into the role of COUP-TFII in prostate tumorigenesis. PC3 Cells were transfected with siRNA (Control or COUP-TFII siRNA) duplexes (40 nM) and total RNA was isolated 48 hours later.
Project description:Arbuscular mycorrhiza (AM) interactions between plants and Glomeromycota fungi primarily support phosphate aquisition of most terrestrial plant species. To unravel gene expression during early stages of Medicago truncatula root colonization by AM fungi, we used genome-wide transcriptome profiling based on mycorrhizal root fragments enriched for early fungal infection stages. We used Medicago GeneChips to detail the global programme of gene expression in response to early stages of colonization by arbuscular mycorrhizal fungi and identified genes differentially expressed during these early stages. Medicago truncatula GFP-HDEL hairy roots (genotypes A17 and DMI3) were grown in vertically-oriented petri dishes, incubated at 26M-BM-0C and inoculated with 8 Gigaspora margarita spores, which were positioned between the lateral roots. G.margarita spores germinated in 2 to 4 days. Hyphopodia were observed after 5-6 days. Root fragments which reacted to the fungal contact were collected and frozen. Non-inoculated control root fragments were harvested at a comparable age.
Project description:Group living animals must be able to express different behavior profiles depending on their social status. This implies that the same genotype may translate into different behavioral phenotypes through socially driven differential gene expression. Here we show for the first time that what triggers the switch between status-specific neurogenomic states is not the objective structure of the social interaction but rather the subjectsM-bM-^@M-^Y perception of its outcome. For this purpose we had male zebrafish fight either a real opponent or their own image on a mirror. Massive changes in the brain transcriptome were observed in real opponent fighters, which experience either a victory or a defeat. In contrast, mirror fighters, which had no information on fight outcome despite expressing aggressive behavior, failed to activate a neurogenomic response. These results indicate that, even in cognitively simple organisms such as zebrafish, neurogenomic responses underlying changes in social status rely on cognitive appraisal. Brain samples from zebrafish, Danio rerio were collected after experimental manipulations generated 4 phenotypes regarding social experience: mirror fighters (M), winners of a real opponent fight (W), losers of a real opponent fight (L); and socially isolated fish (I). After 30 minutes of experimental manipulation animals were anesthetized with a lethal dose of MS-222 (1000-1500 mg/l) and decapitated. Brains were rapidly collected, homogenized and RNA extracted following standard methods of RNeasy Lipid Tissue Mini Kit, Qiagen. RNA was then treated with DNase (RNase-free DNase set, Qiagen) to remove possible contaminations with genomic DNA and concentration and purity was estimated by spectrophotometric absorbance in a NanoDrop ND-1000 UV-Vis Spectrophotometer (Nano-Drop Technologies).
Project description:Nitrogen assimilation in plants is a tightly regulated process that integrates developmental and environmental signals. The legume-rhizobial symbiosis results in the formation of a specialized organ called root nodule, where the rhizobia fixes atmospheric nitrogen into ammonia. Ammonia is assimilated by the plant enzyme glutamine synthetase, which is specifically inhibited by PPT. The expression of key genes related to the regulation of root nodule metabolism will likely be affected by glutamine synthetase inhibition. We used microarrays to detail the global programme of gene expression in response to Glutamine synthetase inhibition in root nodules and identified genes differentially expressed over a time course. Medicago truncatula nodulated plants (20 days post inoculation) were treated with 0.25 mM of PPT. Root nodules were harvested at 4, 8 and 24 hours after PPT application. As a control, root nodules collected just before PPT application were used (PPT 0h). Three biological replicates consisting of pools of root nodules harvested from five distinct plants were used for RNA extraction and hybridization on Affymetrix GeneChips.
Project description:Human ES cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are usually generated and maintained on living feeder cells like mouse embryonic fibroblasts or on a cell-free substrate like Matrigel. For clinical applications, a quality-controlled, xenobiotic-free culture system is required to minimize risks from contaminating animal-derived pathogens and immunogens. We previously reported that the pericellular matrix of decidua-derived mesenchymal cells (PCM-DM) is an ideal human-derived substrate on which to maintain hiPSCs/hESCs. In this study, we examined whether PCM-DM could be used for the generation and long-term stable maintenance of hiPSCs. Decidua-derived mesenchymal cells (DMCs) were reprogrammed by the retroviral transduction of four factors (OCT4, SOX2, KLF4, c-MYC) and cultured on PCM-DM. The established hiPSC clones expressed alkaline phosphatase, hESC-specific genes and cell-surface markers, and differentiated into three germ layers in vitro and in vivo. At over 20 passages, the hiPSCs cultured on PCM-DM held the same cellular properties with genome integrity as those at early passages. Global gene expression analysis showed that the GDF3, FGF4, UTF1, and XIST expression levels varied during culture, and GATA6 was highly expressed under our culture conditions; however, these gene expressions did not affect the cellsM-bM-^@M-^Y pluripotency. PCM-DM can be conveniently prepared from DMCs, which have a high proliferative potential. Our findings indicate that PCM-DM is a versatile and practical human-derived substrate that can be used for the feeder-cell-free generation and long-term stable maintenance of hiPSCs. Keywords: Induced pluripotent stem cells; Extracellular matrix; Decidua; Mesenchymal cells The microarray study was carried out using Affymetrix Human Genome U133 Plus 2.0 gene expression arrays. Total RNA was extracted from cells with RNeasy (Qiagen), and 100ng of total RNA was used to synthesize aRNA using the 3M-bM-^@M-^Y IVT Express Kit, according to the manufacturerM-bM-^@M-^Ys instructions (Affymetrix Inc., Santa Clara, CA). After aRNA purification, 15 M-NM-<g of aRNA was fragmented and hybridized with a pre-equilibrated GeneChip array (Human Genome U133 Plus 2.0 gene expression array, Affymetrix) at 45M-BM-0C for 16 hours. The GeneChip array was then washed, stained, and scanned according to the manufacturerM-bM-^@M-^Ys instructions. The gene expression data were extracted using Affymetrix Expression Console software.