Evalutation of the effect of ethanol upon gene expression in adult Drosophila melanogaster
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Vance Trudeau
PROVIDER: E-GEOD-3033 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
The effect of a synergistic concentration of a Piper nigrum extract used in conjunction with pyrethrum upon gene expression in Drosophila melanogaster.
Jensen H R HR Scott I M IM Sims S R SR Trudeau V L VL Arnason J T JT
Insect molecular biology 20060601 3
An ethyl acetate extract of Piper nigrum L. (Piperaceae) peppercorns was tested as a synergist for the botanical insecticide pyrethrum. A high synergist ratio of 11.6 against Drosophila melanogaster was obtained for the combination of pyrethrum supplemented with P. nigrum. The effect of this combination was investigated using cDNA microarray analysis of gene expression profiles in D. melanogaster. Treatment of D. melanogaster with pyrethrum alone resulted in a large number of differentially expr ...[more]
Similar Datasets
Project description:This experiment was used to determine the effect of a botanical insecticide upon gene expression profiles in Drosophila melanogaster. Adult female Drosophila (oregon-R strain) were treated with an ethylacetate extract of Piper nigrum (Piperaceae) seeds formulated in 99% ethanol. Treatment was topical, using a Potter's tower to administer a total of 2 mL of a 0.9mg/mL concentration. Control treatment was identical except flies were treated with 99% ethanol as a solvent control. Gene expression was studied four hours post-treatment. The design is a direct comparison between total RNA of treated and untreated insects. Sample size is two and two reverse label hybridizations were done. Each sample is a pool of 240 insects which received the same treatment simultaneously.
2006-01-24 | E-GEOD-3032 | biostudies-arrayexpress
Project description:Enteric pathogens have developed several resistance mechanisms to survive the antimicrobial action of bile. We investigated the transcriptional profile of Vibrio cholerae O1 El Tor strain C6706 under virulence gene inducing conditions, in the presence and absence of bile. Microarray analysis revealed that the expression of 119 genes was affected by bile. The mRNA levels of genes encoding proteins involved in transport was increased in the presence of bile, whereas mRNA levels of genes encoding proteins involved in pathogenesis and chemotaxis was decreased. This study identified genes encoding transcriptional regulators from the TetR family (vexR and breR) and multidrug efflux pumps from the RND superfamily (vexB and vexD [here renamed breB]) that were induced in response to bile. Further analysis regarding vexAB and breAB expression in the presence of various antimicrobial compounds established that vexAB was induced in the presence of bile, SDS or novobiocin, whereas induction of breAB was specific to bile. BreR is a direct repressor of the breAB promoter and is able to autoregulate its own expression, as demonstrated by transcriptional and electrophoretic mobility shift assays (EMSA). Expression of breR and breAB is induced in the presence of the bile salts cholate, deoxycholate or chenodeoxycholate and EMSA showed that deoxycholate is able to abolish formation of BreR-PbreR complexes. We propose that deoxycholate is able to interact with BreR and induce a conformational change that will interfere with its DNA binding ability resulting in breAB and breR expression. These results provide new insight into a transcriptional regulator and a transport system that likely play an essential role in the ability of Vibrio cholerae to resist the action of bile in the host. Keywords: Vibrio cholerae response to bile Three independent experiments were performed for the microarray analysis. From each experiment, RNA was obtained from four different time points and was prepared for hybridization, therefore, a total of 3 slides were analyzed per time point. The growth conditions were as follows; C6706 str2 was grown 15 h in LB medium at 30 degrees C with aeration. The cultures were then diluted 100-fold into AKI medium with, or without, 0.4% crude bile (high bile concentration) and were grown at 37degrees C for 3.5 h stationary followed by 2 h with aeration to induce virulence gene expression. Then the cultures were diluted 100-fold into AKI medium with, or without, 0.02% crude bile (low bile concentration) and were grown at 37 degrees C for 2 h stationary. Samples were obtained from 4 different time points: 2, 4, and 5.5 h from the high bile cultures, and at 2 h from the low bile cultures.
2010-06-05 | E-GEOD-6468 | biostudies-arrayexpress
Project description:Cardiac endothelial RNA from Tie-2 GFP mice exposed to intraperitoneal LPS vs. saline, 4 h. RNA amplified 2 rounds. Experiment and dye reversal with cy5, cy3.
2010-06-09 | E-GEOD-1038 | biostudies-arrayexpress
Project description:Endothelial responses to LPS using endothelial cells freshly isolated from Tie2 GFP animals vs. cultured cell line. This SuperSeries is composed of the SubSeries listed below.
2010-06-09 | E-GEOD-1044 | biostudies-arrayexpress
Project description:Endothelial cells from mice exposed to enviromental tobacco smoke for 1 or 6 weeks.
2010-06-10 | E-GEOD-2090 | biostudies-arrayexpress
Project description:Oxygen lack of various severity can force many organisms to enter into recoverable hypometabolic states. To better understand how organisms cope with oxygen deprivation, our lab had previously shown that when challenged with anoxia, both the nematode Caenorhabditis elegans and embryos of the zebrafish Danio rerio enter into suspended animation, where all life processes that can be observed by light microscopy reversibly halt, pending restoration of oxygen. Here, we show that both sporulating and vegetative cells of the budding yeast Saccharomyces cerevisiae also enter into a similar state of suspended animation when made anoxic on a non-fermentable carbon source. Transcriptional profiling using cDNA microarrays shows upregulation of aerobic metabolism genes in carbon monoxide (CO)-induced anoxia, but not nitrogen (N2) gas-induced anoxia, consistent with the known oxygen-mimetic effects of CO. Our results lead us to propose a model for oxygen-regulated gene expression in yeast where two oxygen-sensitive mechanisms operate simultaneously, such that treatment with N2 results in both mechanisms signaling a lack of oxygen, while treatment with CO results in one sensing mechanism signaling a lack of oxygen, while the other signals an abundance of oxygen. Cells were pregrown on glucose media. Cells were then plated onto nylon membranes on acetate solid media and made anoxic using either pure nitrogen or carbon monoxide. Cells were collected at 15, 30, 45, 60, 120 minutes and 24 hours after initiation of gas exposure. Reference samples were derived from cells on acetate in room air for corresponding time point. Six CO-treated samples were compared to room air references and six nitrogen-treated samples were similarly compared to room air references.
2008-07-08 | E-GEOD-12004 | biostudies-arrayexpress
Project description:Biallelic inactivating mutations of the transcription factor 1 gene (TCF1), encoding hepatocyte nuclear factor 1a (HNF1a), were identified in 50% of hepatocellular adenomas (HCA) phenotypically characterized by a striking steatosis. To understand the molecular basis of this aberrant lipid storage, we performed a microarray transcriptome analysis validated by quantitative RT-PCR, western-blotting and lipid profiling. In mutated HCA, we showed a repression of gluconeogenesis coordinated with an activation of glycolysis, citrate shuttle and fatty acid synthesis predicting elevated rates of lipogenesis. Moreover, the strong dowregulation of L-FABP suggests that impaired fatty acid trafficking may also contribute to the fatty phenotype. In addition, transcriptional profile analysis of the observed deregulated genes in non-HNF1a-mutated HCA as well as in non-tumor livers allowed us to define a specific signature of the HNF1a-mutated HCA. In theses tumors, lipid composition was dramatically modified according to the transcriptional deregulations identified in the fatty acid synthetic pathway. Surprisingly, lipogenesis activation did not operate through SREBP-1 and ChREBP that were repressed. We conclude that steatosis in HNF1a-mutated HCA results mainly from an aberrant promotion of lipogenesis that is linked to HNF1a inactivation and that is independent of both SREBP-1 and ChREBP activation. Finally, our findings have potential clinical implications since lipogenesis can be efficiently inhibited by targeted therapies. Keywords: Disease state analysis In a first experiment, microarray analyses were applied to 8 HNF1-alpha mutated HCA and their corresponding non-tumor livers using cDNA in-house manufactured arrays following a randomized and blinded unbalanced design. RNA labelling, hybridization and analysis of fluorescence was carried out, as described in [Graudens et al., Genome Biol 2006, 7: R19; PMID: 16542501], considering that uneven numbers of samples were randomly allocated to each of the engineers who were not aware of sample phenotypes. To assess data reproducibility and minimize dye bias effects, each of the samples was measured four times, twice with Cy3 and twice with Cy5. To ensure robustness and flexibility in data analysis, a reference design was used with a universal reference sample (Stratagene, USA) serving as a baseline for the comparisons of tumor samples. Hybridizations were performed onto an 11K human array (11K_VJF-ARRAY, GPL3282), which provides a genome-wide coverage of functional pathways. Raw data were obtained using the ArrayVisionM-bM-^DM-" 7.0 software (Imaging Research Inc., USA); the resulting 3.2x106 hybridization data points collected from 32 arrays were stored in a MIAME-compliant database and pre-processed for normalization and filtering as described in [Graudens et al., Genome Biol 2006, 7: R19; PMID: 16542501]. In a second experiment, HG-U133A Affymetrix GeneChipTM arrays were used to compare the expression profiles of 5 HNF1-alpha mutated HCA and 4 non related non-tumor livers. RNA labelling, hybridization and analysis were carried out following the manufacturerM-bM-^@M-^Ys instructions(Affymetrix, Santa Clara, CA). Raw data were obtained by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Santa Clara, USA); the resulting raw numerical data (CEL files) - available as supplementary files - collected from 9 Affymetrix GeneChips were pre-processed for normalization and filtering as described in [Rebouissou et al., J Biol Chem 2007, in press; PMID: 17379603]. A platform-dependant statistical comparison was performed considering HNF1 alpha-mutated HCA versus non tumor liver tissues, using multiple testing procedures to evaluate statistical significance for differentially expressed genes, as described in [Graudens et al., Genome Biol 2006, 7: R19; PMID: 16542501] and in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, in press; PMID: 17379603]. Thus, a combined cross-platform analysis was done considering the UGCluster Identifiants as a common primary key (Unigene Build184-June05). Additional information on the procedures is provided in the supplemental experimental procedures in [Rebouissou et al., J Biol Chem 2007, in press; PMID: 17379603].
2007-05-01 | E-GEOD-7473 | biostudies-arrayexpress
Project description:Yeast cells can be affected during their growth to several stress conditions. One of the most known and characterised is the osmotic stress and most of the studies about osmotic sterss response in yeast have been focused on salt or sorbitol stress. However, during yeast growth in industrially relevant processes (for instance throughout alcoholic fermentation on the must to produce alcoholic beverages) the osmotic stress is mainly due to the high sugar(in particular glucose) concentration (200-250 g/L). In this study we want to know the transcriptional response of the Saccharomyces cerevisiae when it was grown in a medium with high glucose concentration. For this aim we have grown yeast in YP medium containing 2% of glucose in cultures overnight and after that we diluted this cultures to an OD600 of 0.1 in two differents mediums: YP containing 2% or 20% of glucose.One hour later of inoculation we collect the cells and quikly frozen in liquid nitrogen. We extracted the total mRNA of the cells and after that we did the microarrays, comparing cells were grown in YP2 media against the cells were grown in YP20 media.
2011-03-21 | E-GEOD-13703 | biostudies-arrayexpress
Project description:Pentylenetetrazol (PTZ)-induced kindling in rodents is an established model of epileptogenesis. The molecular basis of the associated long-term plasticity is however not clear. Further, rodent models of kindling plasticity are not amenable to large-scale screening of compounds for identifying antiepileptogenic drugs. In this context, we have developed a fly model of chronic PTZ- and withdrawal-induced behavioral plasticity. In our model, the chronic treatment is given for 7 days, followed by 7 day long withdrawal. Gene expression profiles of fly heads secondary to chronic PTZ were examined to identify molecular correlates of behavior in our model. Expression profiling of fly heads at three time points in the 7 day long chronic PTZ - 12 hrs, 2nd day, and 7th day - showed a dynamic and widespread alteration of various functional categories of genes. Keywords: Time Series D. melanogaster Oregon-R wild type flies were grown in standard fly medium consisting of agar-agar, maize powder, brown sugar, dried yeast, and nipagin. The cultures were grown at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Three to four days old unmated adult males were grown in either normal food (NF) or food containing 8 mg/ml of PTZ for seven days. Following this, the control and PTZ treated flies were shifted to vials containing normal food and maintained further for seven days. Each vial contained 30 flies in the beginning of the treatment. Heads were harvested at three time points during PTZ treatement - 12hrs, 2nd day, and 7th day. Flies frozen in liquid nitrogen were shaken and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, every two of which represented a single parallel set of treatment in which four vials contained NF treated control flies, and four PTZ exposed individuals, during treatment or withdrawal period, using TRI REAGENT (Sigma) according to the manufacturerM-bM-^@M-^Ys protocol. Double stranded cDNA was synthesized from 10 M-BM-5g of total RNA using Microarray cDNA Synthesis Kit (Roche). The cDNA was purified using Micorarray Target Purification Kit (Roche), according to the manufacturerM-bM-^@M-^Ys protocol. Each of the four sets of control and treated cDNA samples, belonging to the four biological replicates, was used for labeling with either Cy3 or Cy5 dyes (Amersham Biosciences) using Microarray RNA Target Synthesis Kit T7 (Roche). The labeled products were purified by Microarray Target Purification Kit (Roche). The Cy3 and Cy5 labeled two cRNA samples of each biological replicate were pooled together, precipitated, washed, air-dried, and dissolved in 18MM-NM-) RNAase free water (Sigma). Dye swapping was accomplished by hybridizing two arrays with NF control as Cy3- and PTZ treated as Cy5- labeled sample, and the rest two as the opposite, NF as Cy5- and drug treated as Cy3- labeled sample. The labeled product was mixed with hybridization solution containing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma). The hybridization mixture was denatured at 65M-BM-:C and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by a coverslip (ESCO, Portsmouth, USA) and hybridization was allowed to take place in hybridization chamber (Corning) at 37M-BM-:C for 16 hrs. Following hybridization, the coverslips were removed in a solution containing 1X SSC and 0.1% SDS at 50M-BM-:C, and the slides washed in 1X SSC and 0.1% SDS (three times for 15 minutes each) in a coplin jar at 50M-BM-:C with occasional swirling and then transferred to 1X SSC and washed with gentle swirling at room temperature (twice for 15 minutes each). Slides were given a final wash in 0.1X SSC for 15 minutes and then liquid was quickly removed from the slide surface by spinning at 600 rpm for 5 minutes. Slides were scanned at 10M-BM-5m resolution in GenePix 4000A Microarray Scanner (Molecular Devices). The preprocessing and quantification of the 16 bit TIFF images were carried out using Gene Pix Pro 6.0 software (Molecular Devices). Ratio based normalization was performed using Acuity 4.0 software (Molecular Devices). All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), had relatively uniform intensity and uniform background (Rgn R2 (635/532) >= 0.6) and were detectable above background (SNR >= 3). Analyzable spots in at least three of the four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations.
2007-10-01 | E-GEOD-7120 | biostudies-arrayexpress
Project description:We recently developed a fly model of pentylenetetrazol (PTZ)-induced long-term behavioral plasticity. Pharmacological validation suggests this model to be kindling-like. Hence, our model is of relevance in understanding the molecular pathogenesis of epileptogenesis as well as in screening potential antiepileptogenic agents. Levetiracetam (LEV) is considered to have antiepileptogenic activity. Our fly model also predicted similar activity in LEV. Since the mechanism of action of LEV is not clearly known, we have examined the gene expression profiles of fly heads secondary to three days long chronic LEV treatment in Drosophila. Our results provide novel insights in to the drug’s mode of action. Keywords: Drug Response Oregon-R wild type D. melanogaster was grown in standard fly medium consisting of agar-agar, maize powder, brown sugar, dried yeast, and nipagin. Flies were cultured at 24 +/- 1oC, 60% RH, and 12 hrs light (9 AM to 9 PM) and 12 hours dark cycle. Seven to ten days old unmated adult males were grown in either normal food (NF) or food containing 5 mg/ml of LEV for three days. Each culture vials contained 30 flies. Flies frozen in liquid nitrogen were agitated and the heads collected using cooled sieves. Total RNA was isolated from eight pools of frozen heads, every two of which represented a single parallel set of treatment in which four vials contained NF treated control flies, and four LEV treated individuals, using TRI REAGENT (Sigma) according to the manufacturer’s protocol. Double stranded cDNA was synthesized from 10 µg of total RNA using Microarray cDNA Synthesis Kit (Roche), and the cDNA purified using Micorarray Target Purification Kit (Roche), according to the manufacturer’s protocol. Each of the four sets of NF control and LEV treated cDNA samples, belonging to the four biological replicates, was used for labeling with either Cy3 or Cy5 dyes (Amersham Biosciences) using Microarray RNA Target Synthesis Kit T7 (Roche). The labeled products were purified by Microarray Target Purification Kit (Roche). The Cy3 and Cy5 labeled two cRNA samples of each biological replicate were pooled together, precipitated, washed, air-dried, and dissolved in 18MΩ RNAase free water (Sigma). Dye swapping was accomplished by hybridizing two arrays with NF control as Cy3- and LEV treated as Cy5- labeled sample, and the rest two as the opposite, NF as Cy5- and drug treated as Cy3- labeled sample. The labeled product was mixed with hybridization solution containing hybridization buffer (DIG Easy Hyb; Roche), 10mg/ml salmon testis DNA (0.05 mg/ml final concentration, Sigma) and 10mg/ml yeast tRNA (0.05 mg/ml final concentration, Sigma). The hybridization mixture was denatured at 65ºC and applied onto cDNA microarray slides (D12Kv1, CDMC, Toronto). The slides were covered by a coverslip (ESCO, Portsmouth, USA) and hybridization was allowed to take place in hybridization chamber (Corning) at 37ºC for 16 hrs. Following hybridization, the coverslips were removed in a solution containing 1X SSC and 0.1% SDS at 50ºC, and the slides washed in 1X SSC and 0.1% SDS (three times for 15 minutes each) in a coplin jar at 50ºC with occasional swirling and then transferred to 1X SSC and washed with gentle swirling at room temperature (twice for 15 minutes each). Slides were given a final wash in 0.1X SSC for 15 minutes and then liquid was quickly removed from the slide surface by spinning at 600 rpm for 5 minutes. Slides were scanned at 10µm resolution in GenePix 4000A Microarray Scanner (Molecular Devices). The 16 bit TIFF images were preprocessed and quantified using Gene Pix Pro 6.0 software (Molecular Devices). Ratio based normalization was performed using Acuity 4.0 software (Molecular Devices). All Spots with raw intensity less then 100U and less then twice the average background was ignored during normalization. Normalized data was filtered for the selection of features before further analysis. Only those spot were selected which contained only a small percentage (<3) of saturated pixels, were not flagged bad or found absent (flags >= 0), and were detectable above background (SNR >= 2). Analyzable spots in at least three of the four biological replicates performed were retrieved for downstream analysis using Significance Analysis of Microarrays (SAM 3.0, Excel Add-In, Stanford) under the conditions of one class response and 100 permutations
2007-10-03 | E-GEOD-7488 | biostudies-arrayexpress