Expression data from the T-DNA insertion line atpip1;2-1
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE62167 | GEO | 2015/01/10
SECONDARY ACCESSION(S): PRJNA263338
REPOSITORIES: GEO
Similar Datasets
Project description:Some aquaporins do not show a pronounced function as water diffusion facilitators but act as small molecule transport facilitators for substances such as urea, glycerol, boron or gases such as CO2 . Transcriptome analysis provided distinguishable, specific profiles for water stress or for conditions of increased or decreased CO2 concentrations We used Affymetrix microarray analysis to elucidate the function of the aquaporin AtPIP1;2 gene A T-DNA insertion line atpip1;2-1 was used for RNA extraction and further microarray analysis based on the Affymetrix platform. The transcriptome of the atpip1;2-1 line was compared to the wild type (N-60000).
2015-01-10 | E-GEOD-62167 | biostudies-arrayexpress
Project description:Insufflation of the colon, usually with room air, is necessary to distend the lumen for exploration. Carbon dioxide (CO2) insufflation instead of room air insufflation (AI) has been shown to decrease symptoms of abdominal pain or discomfort during the procedure and particularly during the following 24 hours. CO2 is is rapidly absorbed by the intestinal mucosa and exhaled through respiration. AI colonoscopy has usually been the reference standard to compare colonoscopy using CO2 insufflation. In two recent articles AI was compared to either CO2 insufflation and Water-aided colonoscopy (WAC), which entails infusion of water to facilitate insertion to the cecum.
WAC can be categorized broadly in Water Immersion (WI) and Water Exchange (WE). In WI water is infused during the insertion phase of colonoscopy, with removal of infused water predominantly during withdrawal. Occasional use of insufflation may be allowed. WE entails complete exclusion of insufflation, removal of residual colonic air pockets and feces, and suction of infused water predominantly during insertion to minimize distention. During the withdrawal phase insufflation is used to distend the colonic lumen.
In the WAC arms of the two mentioned articles the insertion method used was WI, with infusion of water at room temperature or at 37°C. During withdrawal, air insufflation or either air or CO2 insufflation were employed.
Compared to AI, CO2 insufflation and WI (using room air insufflation or CO2 insufflation during withdrawal) were effective in both studies in decreasing sedation requirement, pain and tolerance scores, with patients’ higher willingness to repeat the procedure.
Until now no direct comparison has been made within a single study about pain score during colonoscopy using AI, CO2 insufflation, WI/CO2, WE/CO2, WI/AI and WE/AI.
In this study we test the hypothesis that, compared to AI, CO2 insufflation and WAC/CO2-AI methods will decrease pain score during colonoscopy, with reduction of sedation requirement, and that WE will achieve the best result. This comparative study has also the aim to test the respective peculiarities of each method.
| 2152551 | ecrin-mdr-crc
Project description:Background: The mammalian kidneys maintain salt and water homeostasis for proper electrolyte balance and hydration. As the glomerular filtrate passes through the nephron and into the renal medulla, electrolytes, water, and urea are reabsorbed through the concerted actions of solute carrier channels and aquaporins located at various positions along the nephron and in the outer and inner medulla. Renal epithelial cells develop from Pax2 positive proliferating stem cells that suppress Pax2 expression once differentiated into mature proximal and distal tubules, but continue to express the related Pax8 protein. The collecting tubules and renal medulla are derived from a Pax2 positive ureteric bud epithelia that continue to express Pax2 and Pax8 in adult kidneys. Despite the necessity for Pax2 in renal development, functions for Pax2 or Pax8 in adult renal epithelia have not been established. Methods: In this report, we deleted either Pax2, Pax8, or both genes in adult mice and examined the phenotypes and changes in gene expression patterns. The mechanism of Pax8 mediated activation of potential target genes was described in inner medullary collecting duct cells. Results: Mice with induced deletions of both Pax2 and Pax8 exhibit severe polyuria that can be attributed to significant changes in the expression of solute carriers, such as the urea transporter UTA1, and aquaporins within the inner and outer medulla. Furthermore, Pax8 expression is induced by high salt in collecting duct cells and activates the UTA1 gene by recruiting a histone methyltransferase complex to the promoter. Conclusions: These data uncover novel functions for Pax proteins, in adult renal epithelia, that are essential for retaining water and concentrating urine.
2019-12-05 | GSE141455 | GEO
Project description:Plants have evolved sophisticated systems to respond to environmental changes, and growth arrest is a common strategy to enhance stress tolerance. Despite the growth-survival tradeoffs is essential for shaping plant productivity, the mechanisms balancing growth and survival remain largely unknown. Aquaporins play a crucial role in growth and stress responses by controlling water transport across membranes. Here, we present that RhPIP2;1, an aquaporin from rose (Rosa sp.), interacts with a membrane-tethered MYB protein, RhPTM. Water deficiency triggers nuclear translocation of RhPTM C-terminus. Silencing of RhPTM causes continuous growth under drought stress, and a consequent decrease in survival rate. RNA-seq indicates that RhPTM influences expression of genes related to carbohydrate metabolism. Water deficiency induces phosphorylation of RhPIP2;1 at Ser273, which is sufficient to promote nuclear translocation of RhPTM C-terminus. These results indicate that RhPIP2;1-RhPTM module serves as a critical player to orchestrate the tradeoff between growth and stress survival in rose.
2019-01-16 | PXD011943 | Pride
Project description:Plants have evolved sophisticated systems to respond to environmental changes, and growth arrest is a common strategy to enhance stress tolerance. Despite the growth-survival tradeoffs is essential for shaping plant productivity, the mechanisms balancing growth and survival remain largely unknown. Aquaporins play a crucial role in growth and stress responses by controlling water transport across membranes. Here, we present that RhPIP2;1, an aquaporin from rose (Rosa sp.), interacts with a membrane-tethered MYB protein, RhPTM. Water deficiency triggers nuclear translocation of RhPTM C-terminus. Silencing of RhPTM causes continuous growth under drought stress, and a consequent decrease in survival rate. RNA-seq indicates that RhPTM influences expression of genes related to carbohydrate metabolism. Water deficiency induces phosphorylation of RhPIP2;1 at Ser273, which is sufficient to promote nuclear translocation of RhPTM C-terminus. These results indicate that RhPIP2;1-RhPTM module serves as a critical player to orchestrate the tradeoff between growth and stress survival in rose.
2019-01-16 | PXD011942 | Pride
Project description:Plasma membrane intrinsic proteins (PIPs) are one subfamily of aquaporins that mediate the transmembrane transport of water. To reveal their function in poplar, we generated transgenic poplar plants in which the translation of PIP genes was downregulated by RNA interference investigated these plants with a comprehensive leaf plasma membrane proteome and physiome analysis. First, inhibition of PIP synthesis strongly altered the leaf plasma membrane protein composition. Strikingly, several signaling components and transporters involved in the regulation of stomatal movement were differentially regulated in transgenic poplars. Furthermore, hormonal crosstalk related to abscisic acid, auxin and brassinosteroids was altered, in addition to cell wall biosynthesis/cutinization, the organization of cellular structures and membrane trafficking. A physiological analysis confirmed the proteomic results. The leaves had wider opened stomata and higher net CO2 assimilation and transpiration rates as well as greater mesophyll conductance for CO2 (gm) and leaf hydraulic conductance (Kleaf). Based on these results, we conclude that PIP proteins not only play essential roles in whole leaf water and CO2 flux but have important roles in the regulation of stomatal movement.
2015-08-10 | PXD002544 | Pride
Project description:Poplars are known to be highly tolerant species to boron toxicity and accumulation. However, genes and molecular networks responsible in boron toxicity tolerance have not been investigated yet. Therefore, we performed a pot experiment with 20 black poplar clones collected from the vicinity of boron mines and polluted areas to investigate its potential role in phytoremediation and to select the most boron toxicity tolerant genotype. Trees were treated with irrigation water containing seven elevated boron concentrations from 0 to 160 ppm. Then a microarray based comparative transcriptome profiling was conducted to identify boron toxicity regulated genes responsible in defence responses of black poplar. The results of the study indicated that black poplar is quite suitable for phytoremediation of boron pollution. It could resist 15 ppm soil B content and < 1600 mg/kg boron accumulation in leaves which are highly toxic concentrations for almost all agricultural plants. Transcriptomics results of study revealed totally 1625 and 1419 altered probe sets under boron toxicity in leaf and root tissues, respectively. The highest induction were recorded for the probes sets annotated to tyrosine aminotransferase, ATP binding cassette transporters, glutathione S transferases and metallochaperone proteins. Strong up regulation of these genes attributed to internal excretion of boron into the cell vacuole and existence of detoxification processes in black poplar. Many candidate genes functional in signalling, gene regulation, antioxidation, boron uptake, transport and detoxification processes were also identified in the current study. This is the first transcriptomic study identifying boron toxicity regulated poplar genes and their potential role in boron toxicity tolerance.
2016-06-28 | GSE83745 | GEO
Project description:Smoke released from burning vegetation functions as an important environmental signal promoting the germination of many plant species following a fire . It not only promotes the germination of species from fire-prone habitats, but several species from non-fire-prone areas also respond, including some crops. Bioactivity-guided fractionation of smoke-water led to the identification of a highly active butenolide compound, 3-methyl-2H-furo[2,3-c]pyran-2-one. Several hypotheses have arisen regarding the molecular background of smoke and butenolide action. Contrary to the efforts to unravel the mode of action of smoke, the mechanism is still largely unknown. In this paper we demonstrate that although smoke-water and butenolide treatment of maize kernels results in a similar physiological response, the gene and protein expression patterns are quite different. Treatment with smoke-water enhanced the ubiquitination of proteins and activated protein-degradation-related genes. This effect was completely absent from butenolide-treated kernels, in which a specific aquaporin gene was distinctly upregulated. These findings indicate that other bioactive compounds present in smoke-water may act together, leading to accelerated protein turnover. The results highlight the importance of protein degradation and aquaporins in the seed germination process. Besides their obvious use in the sustainable agricultural practice, smoke and butenolide can be used in studies to gain further insight into the transcriptional changes during germination.
2009-08-24 | GSE17484 | GEO
Project description:Poplars are known to be highly tolerant species to boron toxicity and accumulation. However, genes and molecular networks responsible in boron toxicity tolerance have not been investigated yet. Therefore, we performed a pot experiment with 20 black poplar clones collected from the vicinity of boron mines and polluted areas to investigate its potential role in phytoremediation and to select the most boron toxicity tolerant genotype. Trees were treated with irrigation water containing seven elevated boron concentrations from 0 to 160 ppm. Then a microarray based comparative transcriptome profiling was conducted to identify boron toxicity regulated genes responsible in defence responses of black poplar. The results of the study indicated that black poplar is quite suitable for phytoremediation of boron pollution. It could resist 15 ppm soil B content and < 1600 mg/kg boron accumulation in leaves which are highly toxic concentrations for almost all agricultural plants. Transcriptomics results of study revealed totally 1625 and 1419 altered probe sets under boron toxicity in leaf and root tissues, respectively. The highest induction were recorded for the probes sets annotated to tyrosine aminotransferase, ATP binding cassette transporters, glutathione S transferases and metallochaperone proteins. Strong up regulation of these genes attributed to internal excretion of boron into the cell vacuole and existence of detoxification processes in black poplar. Many candidate genes functional in signalling, gene regulation, antioxidation, boron uptake, transport and detoxification processes were also identified in the current study. This is the first transcriptomic study identifying boron toxicity regulated poplar genes and their potential role in boron toxicity tolerance. Total RNA used in microarray experiment was isolated from the leaves and roots of black poplar clone; N.92.237 which accumulated the highest amount of boron its tissues. Total RNA used in the microarray experiment was isolated from leaves and roots of three black poplar saplings grown in ~ 2 ppm (control) and ~ 15 ppm (toxic) soil B contents. RNA isolation was made according to Lithium chloride precipitation method described in Chang et al. (1993). These three isolated RNAs (biological replicates) for each tissue loaded onto three Affymetrix poplar Gene Chips (technical replicates). Totally, 12 GeneChips (2 tissues Ã? 2 different B treatment Ã? 3 biological replicates) were used for transcriptional analysis.
2016-06-28 | E-GEOD-83745 | biostudies-arrayexpress
Project description:The pyrenoid, a single microcompartment of the chloroplasts of most algae and hornworts, is the major site of CO2 fixation. To compensate the limited availability of CO2 in aquatic environments due to slower CO2 diffusion in water than air, the RubisCO-containing pyrenoid is involved in a carbon concentrating mechanism (CCM) and promotes the carboxylase activity rather than the oxygenase activity of RubisCO, the Calvin-Benson cycle enzyme catalyzing the first step of CO2 fixation. Data in the literature suggest that pyrenoid can have other functions in addition to CO2 fixation. To decipher its functions, the characterization of the pyrenoid proteome in the microalga Chlamydomonas reinhardtii was undertaken. Pyrenoid-enriched fractions from two independent biological cultures (sample1 and sample2) were obtained from cells (WT-cell) or isolated chloroplasts (WT-cp) either from the wild-type (WT) strain or from pyrenoid-deficient Chlamydomonas strains (MX-CW15 and SS-AT) and analyzed by nLC-MS/MS. Substractive proteomic analysis allowed the identification of contaminant proteins and the characterization of the pyrenoid proteome.
2018-02-28 | PXD004509 | Pride