Wine yeast EC1118 and CSM comparative transcriptomics during synthetic grape juice fermentation MS300 at day 6
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ABSTRACT: CSM is a commercial wine yeast with a long chronological life span, while commercial strain EC1118 displays a short life span in laboratory synthetic complete medium SC. Our aim is compare their expression profile on a high sugar fermentation From a preculture of two days in YPD, MS300 was innoculated at 10exp6 cells/mL in filled-in 50 mL conical centrifuge tubes and they were cultivated at 24ºC with mild shaking for 6 days.
Project description:Rooted plantlets of Populus euphratica were transferred to aerated hydroculture with Long Ashton nutrient solution, grown for 3.5 months at 22°C, 150 µmol m-2 s-1 photosynthetically active radiation with a photoperiod of 16h light. After reaching an average height of 0.83 m, the media was supplemented with 150 mM NaCl (Salt-treated) or maintained under control conditions (control). During the experimental phase, light was continuously supplied to avoid interference of light/dark transitions. <br>Roots and leaves of six plants were harvested separately after 3h, 6h, 12h, and 24h of salt exposure and of controls at the corresponding time points (= 48 plants per experiment). The material of each harvest of 6 plants was pooled, yielding one leaf and one root sample of controls and one leaf and one root sample of salt-treated plants, respectively (=16 samples per experiment).<br>The experiment was performed three times yielding three biological replications (=48 samples in total).<br>After extraction of RNA and cDNA synthesis, each extract was labelled with Cy3 and Cy5, respectively (yielding 96 labelled extracts). Extracts from e.g. 3h-salt-treated leaf exp. 1 (cy3) was hybridized with 3h-control leaf exp.1 (cy5) with microarrays (UHPB-P.euphratica-10K-5; A-MEXP-93)containing unique 7,662 ESTs of P. euphratica from stress-induced cDNA libraries (Brosche et al., Genome Biology 2005, 6:R101). Dye swap was perfomed, thus usually yielding 6 arrays per timepoint and plant tissue (3 biological, 3 technical replicates). In some cases hydridizations were not successfull. Therefore, for roots harvested at timepoints 12h and 24 h only 4 arrays per timepoint were used. For roots harvested after 3h an additional mixed sample of all 3 biological replicates was performed. One leaf array at 6 h was not sucessfull. Therefore, residual labelled extract from salt treated plants of exp1 was hydridized with controls at 6h from exp.2. <br>
Project description:Perfluorooctane sulfonate (PFOS) has been manufactured for over 50 years in increasing quantities and has been used for several industrial and commercial aims. Due to the persistence and the bioaccumulation of this pollutant, it can be found worldwide in wildlife and humans. Biochemical effects of PFOS exposure are mainly studied in mammalian model species and information about effects on fish species remain largely scarce. This lack of toxicity data points out that there is an urgent need for the mechanistic molecular understanding of the mode of action of this pollutant. In the present study, common carp (Cyprinus carpio) was exposed through water for 14 days at concentrations of 0.1; 0.5 and 1 mg/l PFOS. Liver was selected as target tissue. Custom microarrays were constructed from cDNA libraries obtained with Suppression Subtractive Hybridization-Polymerase chain reaction (SSH-PCR) experiments. Microarray data revealed that the expression of several genes in the liver was influenced by PFOS exposure and real-time PCR was used to confirm these gene expression changes. The affected genes were mainly involved in energy metabolism, reproduction and stress response. Furthermore, the relative condition factor and the hepatosomatic index of the exposed fish were significantly lower after 14 days of exposure as well as the available glycogen reserves. At all levels of biological organization, indications of a trade-off between the metabolic cost of toxicant exposure on one hand and processes vital to the survival of the organism on the other hand were seen. Our results support the prediction that increases in energy expenditure negatively affects processes vital to the survival of an organism, such as growth. Keywords: PFOS, common carp, microarray, condition factor, energy reserves, metabolic cost There were 3 biological replicates for each exposure concentration. For each biological replicate control versus exposed hybridizations were carried out. The mean of the biological replicates was calculated for the differentially expressed genes.
Project description:A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores. Three Biological replicates were done of which the third replicate was a dye-swap. In total 12 samples were analyzed. Each array constituted one replicate making six arrays for the whole experiment.
Project description:22 day old Arabidopsis Col-0 plants were sprayed with 0.5 mM sodium nitroprusside (SNP), corresponding controls were sprayed with water, and leaves harvested 3 hours after spraying and frozen in liquid nitrogen.
Project description:We are studying the tree P. euphratica growing in its natural habitat in the Negev desert in Israel. We have used leaf RNA samples from trees growing from four different areas in the desert valley Ein Avdat with contrasting growth conditions, with the primary factor being how much water the trees have access to. Area A trees grow close to a stream. Area B trees are further away from the stream. Area C trees are growing on a slope with no water. Parking place trees grow at a parking place (1km from Area A, B and C) where there is a water irrigation system, and these trees are regularly watered once a week. The control sample in each hybridization is always RNA isolated from a pool of 5 trees from the parking place. The hybridizations are comparing the following: Area A -- parking place Area B -- parking place Area C -- parking place Each hybridization is done with a dye swap and three different biological repeats for a total of 18 hybridizations.
Project description:Comparative transcriptome analysis in various oxygen concentrations of wild type and fixJ mutant strains of Sinorhizobium meliloti.
Project description:This SuperSeries is composed of the following subset Series: GSE25545: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (LB medium vs. iron-limited condition) GSE25546: Prediction, microarray and Northern blot analyses identify new intergenic small RNAs in Aliivibrio salmonicida (wild type vs. LitR mutant) Refer to individual Series