Compression Xylem vs. Opposite Xylem
Ontology highlight
ABSTRACT:
ORGANISM(S): Pinus pinaster
SUBMITTER: Rocio Bautista
PROVIDER: E-GEOD-37789 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification. Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.
2012-05-05 | E-GEOD-37736 | biostudies-arrayexpress
Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification. Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.
2012-05-05 | E-GEOD-37678 | biostudies-arrayexpress
Project description:The objective of this study was to identify porcine genes which expression was affected in vitro stimulation with LPS from Salmonella typhimurium. Microarray experiment was conducted to reveal genes being significantly differentially expressed in LPS stimulated versus unstimulated porcine alveolar macrophages from two from healthy pigs The comparison was done LPS alveolar macrophages versus unstimulated alveolar macrophages sampled from two healthy pigs. The experiment was conducted as common reference design.
2013-12-11 | E-GEOD-53186 | biostudies-arrayexpress
Project description:Sky1 is a Saccharomyces cerevisiae rich serine-arginine (SR) protein-specific kinase and its enzymatic activity is essential in the cytotoxicity caused by cisplatin, although the molecular mechanisms supporting this function are not understood. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin which are dependent or independent of the Sky1 function. The S. cerevisiae strain W303 (MATa ade2-1 can1-100 leu2-3,112 trp1-100 ura3- 52) and its derivative W303-M-NM-^Tsky1 previously described (RodrM-CM--guez- Lombardero et al., 2012) have been used in these analyses. Biological replicates of cultures and treatments were run in triplicate. The yeast cells were pre-cultured over night in 10mL of complete synthetic medium (SD) prepared as previously described (Zitomer and Hall, 1976). The following day the cells were inoculated at initial OD600 of 0.4 in 70 mL SD and grown in 250 mL Erlenmeyer flasks at 30 M-BM-:C and with agitation at 250 rpm. When cells reached OD600 of 0.6, the cultures from each strain were divided in two aliquots of 25 mL (control and cisplatin treatment). A stock solution of cisplatin 6 mM in dimethyl sulfoxide (DMSO) was prepared and the drug was added to the treated cultures at a final concentration of 600 microM. An equivalent volume of DMSO was added to the control cultures. The treatment was done at 30M-BM-:C and with agitation at 250 rpm during four hours in darkness. RNA was extracted from a number of cells corresponding to OD600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturerM-bM-^@M-^Ys instructions. The RIN parameter (RNA Integrity Number) evaluated with the 2100 was near to the value 9 in all the samples. Three different RMA analyses were performed: Analysis 1: GSM1008483-GSM1008488 Analysis 2: GSM1008489-GSM1008494 Analysis 3: GSM1008495-GSM1008500
2014-08-01 | E-GEOD-41094 | biostudies-arrayexpress
Project description:affy_popsec_orleans_poplar - xyleme - This project aims to identify candidate genes for water deficit acclimation and/or adaptation in a tree species: poplar. Due to compelling evidence that transcriptional regulation plays a major role in regulating many biological processes, we will look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in two poplar genotypes of contrasted tolerance to water deficit, at various stages and intensities of stress and simultaneously in whole xylem and cambial zone from young trees. The co-analysis of two genotypes of contrasted tolerance to water deficit should allow to better discriminating genes presenting a potential adaptative character from genes responding passively to the constraint. The consideration of both whole xylem and cambial zone will enable us to discriminate between regulations events originating from very young xylem cells undergoing their first steps of xylem differentiation (cambial zone) compared to whole xylem sample enriched in more differentiated xylem cells and parenchyma ray cells.-Two poplar clones, named Soligo (S) and Carpaccio (C) were submitted to 4 treatments: non-stressed control, severe-drought stress, mild-drought stress and early-drought stress. Two pools of 2 or 3 trees were considered as biological replicates. Two different samples were collected on each individual tree: whole stem xylem (X) and cambial zone plus very young expanding xylem (Y). Total RNAs were extracted from each tree and assemble in pool of 3 or 2 individuals using equimolar ratio for each X and for Y. One affymetrix slide corresponds to one pooled RNA sample (X or Y). A total number of slides : 4 treatments x 2 clones x 2 tissues x 2 biological replicates (pool) = 32 slides, will be done. Keywords: genotype and ecotype comparison,organ comparison,treated vs untreated comparison 32 arrays - poplar
2012-12-15 | E-GEOD-17220 | biostudies-arrayexpress
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison
2011-09-29 | E-GEOD-27063 | biostudies-arrayexpress
Project description:The goal of this experiment is to evaluate the potential for utilising this oligonucleotide microarray in other species and genera of the Pinaceae family by using comparative RNA hybridizations in four different spruces (Picea spp), two pines (Pinus spp.) and a larch (Larix laricina), across two tissues, xylem and phelloderm. One-color comparison of 7 conifer species in 2 tissue types: xylem and phelloderm. Between 4 and 28 biological repetitions per sample type, depending on the species, for a total of 142 slides.
2012-02-16 | E-GEOD-35847 | biostudies-arrayexpress
Project description:The goal of this experiment is to assess tissue preferential transcript accumulation and fold difference between two tissues that support secondary vascular growth in three spruces: Picea glauca, Picea sitchensis and Picea mariana. Tissues compared are secondary xylem (wood forming tissue located on the internal side of the cambial meristem) and phelloderm (composite sample of the phloem and phelloderm tissues located on the outer side of the cambial meristem). One-color comparison of 3 spruce species in 2 tissue types: xylem and phelloderm. 20 biological repetitions per tissue for Picea glauca and 15 for Picea sitchensis and Picea mariana, for a total of 100 slides.
2012-02-18 | E-GEOD-35922 | biostudies-arrayexpress
Project description:affy_rewatering_poplar - rewatering - Biological question (15 lines max): Xylogenesis is a complex process and is highly influenced by environmental factors. Numerous studies have shown xylem structural acclimation to moderate and long-lasting water deficits. A decrease in cell lumen size and an increase in vessel density are generally observed. Other preliminary experiments in our laboratory focusing on a short and progressive drought-rewatering cycle in poplar show a gradual decrease in fibre size with decreasing water availability and an important rise in vessel number with irrigation recovery. This suggests a reorientation during the early stages of cambial derivatives differentiation towards vessel formation. The aim of this study is to characterize global gene expression in young differentiating xylem of poplar in response to a drought-rewatering cycle. Results should provide a comprehensive genomic basis for the xylem structural modifications observed.-The experimental design consisted in a differential water supply. Experiments were done on tilted trees to induce tension wood formation. Trees were regularly irrigated at full capacitance until July 18, 2007, the beginning of the experiment. Two sets of plants were designed. For each set, irrigation was withheld until July 25, 2007. At this time, one of the two sets (treated-sample) was re-irrigated at full capacitance during 14hrs (WDR) while the other one was maintained under water deficit (WD). Samples were collected after the 14hrs for all trees. Keywords: treated vs untreated comparison 6 arrays - poplar
2010-06-16 | E-GEOD-20061 | biostudies-arrayexpress
Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course 10 arrays - poplar
2010-06-16 | E-GEOD-16459 | biostudies-arrayexpress