Transcription profiling of tomato - organ specificity of wax biosynthesis
Ontology highlight
ABSTRACT:
ORGANISM(S): Lycopersicon esculentum
SUBMITTER: Jana Leide
PROVIDER: E-MEXP-2162 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated. MicroTom wild type and lecer6 mutant fruits with a deficiency in a fatty acid beta-ketoacyl-CoA synthase (LeCER6) were used. Identification and characterization of this insertional mutant has been reported previously (Vogg et al., 2004; Leide et al., 2007). According to the developmental stage of the wild type and lecer6 mutant fruits, samples were composed of 5 to 15 whole fruits with seeds being removed (fruit developmental category 'fruit set' and I). Otherwise, samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm (fruit developmental category II to VII). After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2158 | biostudies-arrayexpress
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated (fruit developmental category II). For removal of the epicuticular wax layer a thin film of 1 g ml-1 aqueous gum arabic (Roth, Karlsruhe, Germany) as a fixative was applied to the fruit surface. After 1 h the dried polymer including the outermost epicuticular waxes was mechanically removed. This procedure was repeated once. During this experiment the tomato fruits remained on the tomato plant. Untreated (0 days) and gum arabic stripped tomato fruits harvested 2 days after treatment were compared. Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2163 | biostudies-arrayexpress
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar MicroTom were investigated (fruit developmental category II). After harvest, fruits were immediately utilized or stored in darkness at 25 C until further processing. After 0, 1, 2 or 4 days of storage stem scar tissues of tomato fruits were excised with a scalpel to a depth of approximately 2 mm, immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2151 | biostudies-arrayexpress
Project description:After a standard cultivation program of six weeks, tomato plants (Solanum lycopersicum L.) cultivar MicroTom were grown under different conditions of atmospheric humidity and soil irrigation. The atmospheric humidity was adjusted to 40% and 80%, respectively. To regulate soil moisture, all potted plants were substrate saturated watered once a week. Furthermore, only a group of these plants was irrigated to assure optimally growing conditions (optimal watering conditions), whereas a second group had to cope with little water supply (no watering conditions). Mature green fruits were investigated (fruit developmental category II). Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2165 | biostudies-arrayexpress
Project description:Mature green fruits of the tomato (Solanum lycopersicum L.) cultivar John Baer and Pearson were investigated (fruit developmental category II). John Baer wild type, John Baer LA0063 and Pearson wild type, Pearson 2-303 fruits were used. Tomato mutant plants LA0063 and 2-303 were positional sterile (PS mutants). Samples contained exclusively the fruit peel, which was removed with a scalpel to a depth of approximately 1 mm. After sampling point the plant material was immediately frozen in liquid nitrogen and stored at -80 C until use.
2009-06-09 | E-MEXP-2164 | biostudies-arrayexpress
Project description:gene expression analysis of wild type and DelilaRosea overexpressing microtom tomato fruits
2008-12-01 | E-MEXP-1830 | biostudies-arrayexpress
Project description:We introduced the GAME1i construct into the indeterminate M82 cultivar by crossing, obtaining plants that displayed a phenotype of severe growth retardation, deformed leaves and abortion of flower buds . In addition, leaves of these plants exhibited dark necrotic spots resembling symptoms typically seen after infection of tomato by pathogenic bacteria like Xanthamonas campestris pv. vesicatoria (Xcv) or Pseudomonas syringae pv. tomato (Pst) . As no other tomato lines grown in the same greenhouse at the same time showed similar disease-like symptoms, we hypothesized that silencing GAME1 might mimic induction of disease symptoms in the absence of a pathogen. Indeed, we were able to isolate neither Xcv nor Pst (or other putative pathogens) from GAME1i leaves that displayed necrotic spots. Microarray analysis was performed to examine if the transgene, and possibly, the corresponding changes in the metabolic profile, induced the plant response system at the transcriptional level.
2011-11-28 | E-MEXP-3455 | biostudies-arrayexpress
Project description:Fungal infections are a serious health problem in clinics especially in the immune-compromised patient. Disease ranges from widespread superficial infections like vulvovaginal infections to life-threatening systemic candidiasis. Especially for systemic mycoses only a limited arsenal of antifungals is available. The most commonly used classes of antifungal compounds used include azoles, polyenes and echinocandines. Due to emerging resistance to standard therapy and significant side effects and high costs for several antifungals.,there is a medical need for new antifungals in the clinic and general practice. In order to expand the arsenal of compounds with antifungal activities we previously screened a compound library, using a new type of activity-selectivity (AS) assay analysing both the antifungal activity and the compatibility with human cells at the same time. One compound, ((S)-2-(1-aminoisobutyl)-1-(3-chlorobenzyl) benzimidazole (EMC120B12)), showed high antifungal activity against several species of pathogenic yeasts including C. glabrata and C. krusei, species which are highly refractory to antifungals, especially to the commonly used azoles. Here we could show by transcriptional profiling and sterol analysis that the target of this new antifungal compound is the ergosterol pathway. The effects of EMC120B12 on sterol biosynthesis mimic those of fluconazole, strongly indicating that EMC120B12 also targets ERG11 like the azols. But not only the marker sterol 14 methylergosta 8,24(28) dien 3β,6α diol accumulated in C. krusei under EMC120B12 treatment, but also hitherto unknown related sterols. The novel sterols have a 3β,6α diol structure. Furthermore, this is the first time that a benzimidazole structure has been shown to result in a block of the sterol pathway by accumulating marker sterols connected to ERG11 inactivation. In total, three biological replicates were performed. All experiments were performed as dye swaps. Thus, in total 18 arrays have been hybridzed. Hybridization experiments included an untreated reference sample and a sample of cells treated with either ((1S)-1-[1-(3-chlorobenzyl)-1H-benzimidazol-2-yl]-2-methylpropyl-amine) (EMC120B12), Fluconazole or Nocodazole. The array included one technical replicate of each probe.
2015-06-30 | E-GEOD-64976 | biostudies-arrayexpress
Project description:Cutaneous squamous cell carcinoma (cSCC) is the leading cause of death in recessive dystrophic epidermolysis bullosa (RDEB) patients but remains poorly studied on a proteomic level. We aim to characterize the RDEB-SCC proteome by comparing it to the proteomes of UV-light induced cSCC of non-aggressive and aggressive behavior with which RDEB cSCC share either the well-differentiated morphology or the aggressive behavior, respectively. We applied a direct trypsinization protocol using an acid labile surfactant and label-free quantitation to study formalin-fixed, paraffin-embedded tissues from patients with RDEB cSCC (n=6), low-risk cSCC (n=5) and metastasizing cSCC (n=13) by liquid chromatography tandem-mass spectrometry.
2017-11-27 | PXD006914 | Pride
Project description:BACKGROUND: Prediction models for old-age mortality have generally relied upon conventional markers such as plasma-based factors and biophysiological characteristics. However, it is unknown whether the existing markers are able to provide the most relevant information in terms of old-age survival or whether predictions could be improved through the integration of whole-genome expression profiles. METHODS: We assessed the predictive abilities of survival models containing only conventional markers, only gene expression data or both types of data together in a Vitality 90+ study cohort consisting of n = 151 nonagenarians. The all-cause death rate was 32.5% (49 of 151 individuals), and the median follow-up time was 2.55 years. RESULTS: Three different feature selection models, the penalized Lasso and Ridge regressions and the C-index boosting algorithm, were used to test the genomic data. The Ridge regression model incorporating both the conventional markers and transcripts outperformed the other models. The multivariate Cox regression model was used to adjust for the conventional mortality prediction markers, i.e., the body mass index, frailty index and cell-free DNA level, revealing that 331 transcripts were independently associated with survival. The final mortality-predicting transcriptomic signature derived from the Ridge regression model was mapped to a network that identified nuclear factor kappa beta (NF-?B) as a central node. CONCLUSIONS: Together with the loss of physiological reserves, the transcriptomic predictors centered around NF-?B underscored the role of immunoinflammatory signaling, the control of the DNA damage response and cell cycle, and mitochondrial functions as the key determinants of old-age mortality. The study consisted of 151 nonagenarians who were analyzed for genome-wide transcriptomic mortality predictors in a longitudinal setting.
2015-01-22 | E-GEOD-65218 | biostudies-arrayexpress