Gene expression in hypoxia-tolerant Drosophila melanogaster
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE36507 | GEO | 2015/03/31
SECONDARY ACCESSION(S): PRJNA153457
REPOSITORIES: GEO
Similar Datasets
Project description:Hypoxia plays a key pathogenic role in the outcome of many pathologic conditions. To elucidate how organisms successfully adapt to hypoxia, a population of Drosophila melanogaster was generated, through an iterative selection process, that is able to complete its lifecycle at 4% O2, a level lethal to the starting parental population. Transcriptomic analysis of flies adapted for >200 generations was performed to identify pathways and processes that contribute to the adapted phenotype, comparing gene expression of three developmental stages with generation-matched control flies. A third group was included, hypoxia-adapted flies reverted to 21% O2 for five generations, to address the relative contributions of genetics and hypoxic environment to the gene expression differences. We identified the largest number of expression differences in 0.5-3 hr post-eclosion adult flies that were hypoxia-adapted and maintained in 4% O2, and found evidence that changes in Wnt signaling contribute to hypoxia tolerance in flies. A population of flies able to complete their life cycle at 4% O2 was selected from a starting population of 27 isogenic D. melanogaster lines exposed to increasingly lower O2 levels over many generations. Transcriptomic analysis of adapted flies maintained at 4% O2 or reverted to room air for five generations, and of generation matched naive controls, was performed to better understand changes in gene expression in adapted flies and to investigate the relative contributions of genetics versus environment to these differences.
2015-03-31 | E-GEOD-36507 | biostudies-arrayexpress
Project description:Hypoxia-induced cell injury has been related to multiple pathological conditions. In order to render hypoxia-sensitive cells and tissues resistant to low O2 environment, in this current study, we used Drosophila melanogaster as a model to dissect the mechanisms underlying hypoxia-tolerance. A D. melanogaster strain that lives perpetually in an extremely low-oxygen environment (4% O2, an oxygen level that is equivalent to that over about 4,000 m above Mt. Everest) was generated through laboratory selection pressure using a continuing reduction of O2 over many generations. This phenotype is genetically stable since selected flies, after several generations in room air, survive at this low O2 level. Gene expression profiling showed striking differences between tolerant and naïve flies, in larvae and adults, both quantitatively and qualitatively. Up-regulated genes in the tolerant flies included signal transduction pathways (e.g., Notch and Toll/Imd pathways), but metabolic genes were remarkably down-regulated in the larvae. Furthermore, a different allelic frequency and enzymatic activity of the triose phosphate isomerase (TPI) was present in the tolerant versus naïve flies. The transcriptional suppressor, hairy, was up-regulated in the microarrays and its binding elements were present in the regulatory region of the specifically down-regulated metabolic genes but not others, and mutations in hairy significantly reduced hypoxia tolerance. We conclude that, the hypoxia-selected flies: (a) altered their gene expression and genetic code, and (b) coordinated their metabolic suppression, especially during development, with hairy acting as a metabolic switch, thus playing a crucial role in hypoxia-tolerance. Keywords: genetic bases of hypoxia adaptation 27 isogenic D. melanogaster Lines were pooled and following long-term selection over generations with decreased oxygen level in the culture environment. The differences in gene expression were compared between adapted flies and generation matched naive controls by microarray. Pooled RNA samples from 3rd instar larvae of 27 parental lines were used as common reference.
2010-06-25 | E-GEOD-8803 | biostudies-arrayexpress
Project description:We have used long-term experimental selection over many generations to obtain Drosophila melanogaster strains that can live perpetually in extremely low, normally lethal O2 conditions (4-5% O2). These strains show a dramatic phenotypic divergence from control animals, including a decreased recovery time after anoxia, a higher rate of O2 consumption in hypoxic conditions, and a decrease in body mass due to both decreased cell proliferation and cell size. We used gene expression profiling to identify altered transcript levels in the adapted flies and we show that mutations in many of the corresponding genes confer the ability to survive under extremely low O2 conditions. Keywords: genetic bases of hypoxia adaptation
2007-06-01 | GSE4972 | GEO
Project description:Hypoxia-induced cell injury has been related to multiple pathological conditions. In order to render hypoxia-sensitive cells and tissues resistant to low O2 environment, in this current study, we used Drosophila melanogaster as a model to dissect the mechanisms underlying hypoxia-tolerance. A D. melanogaster strain that lives perpetually in an extremely low-oxygen environment (4% O2, an oxygen level that is equivalent to that over about 4,000 m above Mt. Everest) was generated through laboratory selection pressure using a continuing reduction of O2 over many generations. This phenotype is genetically stable since selected flies, after several generations in room air, survive at this low O2 level. Gene expression profiling showed striking differences between tolerant and naïve flies, in larvae and adults, both quantitatively and qualitatively. Up-regulated genes in the tolerant flies included signal transduction pathways (e.g., Notch and Toll/Imd pathways), but metabolic genes were remarkably down-regulated in the larvae. Furthermore, a different allelic frequency and enzymatic activity of the triose phosphate isomerase (TPI) was present in the tolerant versus naïve flies. The transcriptional suppressor, hairy, was up-regulated in the microarrays and its binding elements were present in the regulatory region of the specifically down-regulated metabolic genes but not others, and mutations in hairy significantly reduced hypoxia tolerance. We conclude that, the hypoxia-selected flies: (a) altered their gene expression and genetic code, and (b) coordinated their metabolic suppression, especially during development, with hairy acting as a metabolic switch, thus playing a crucial role in hypoxia-tolerance. Keywords: genetic bases of hypoxia adaptation
2008-10-01 | GSE8803 | GEO
Project description:One of the critical substances that mammals highly regulate via the respiratory, cardiovascular and neurologic systems is O2. Both low and high O2 levels can induce major morbidities as well as mortality. Indeed, O2 has been often considered as both an elixir and a poison in humans. In current study, we have used an experimental selection approach to generate Drosophila strains that are tolerant to severe hyperoxic environment. Gene expression profiling is then applied to investigate the mechanisms underlying hyperoxia tolerance in the newly generated strains. 27 isogenic D. melanogaster Lines were pooled and following long-term selection over generations with increased oxygen level in the culture environment. The differences in gene expression were compared between adapted flies and generation matched naive controls by microarray.
2010-07-30 | E-GEOD-12160 | biostudies-arrayexpress
Project description:Wild-type Drosophila melanogaster expressing nuclear GFP-KASH fusion protein in photoreceptors for cell type-specific gene expression profiling (Rh1-Gal4>UAS-GFPKASH ; Genotype = w1118;; P{w+mC=[UAS-GFP-Msp300KASH}attP2, P{ry+t7.2=rh1-GAL4}3, ry506) were raised in 12:12h light:dark cycle at 25°C. Flies were aged for 10 or 40 days post-eclosion, and eyes were harvested from male flies for global quantitative proteomic analysis. Significantly changed proteins were identified that may contribute to age-associated retinal degeneration and loss of visual function in the aging Drosophila eye.
2021-07-23 | PXD027090 | Pride
Project description:Due to its aquatic saprophytic lifestyle, the fungus Blastocladiella emersonii seems to be adapted to low aerated environments and thus can be an interesting model of study of the hypoxic stress response. Iron deprivation, a hypoxia-mimicking stimulus due to HIF-1 stabilization, and geldanamycin, that causes HIF-1 depletion by HSP90 inhibition, are helpful parameters to find an evidence of an oxygen-dependent regulatory mechanism in B. emersonii similar to the metazoan HIF-1 pathway. Direct transcript comparison between cells grown under normoxic conditions (70%sat. O2 in air) and cells submitted to oxygen deprivation (direct and gradual) and iron (II) deprivation. It was also compared transcripts of cells submitted to direct 1-hour hypoxia (1%sat. O2) with cells treated with geldanamycin for 1 hour, followed to 1-hour hypoxia (1%sat. O2). There are at least 3 biological replicates (independent harvest) and 2 technical replicates of each array (L - left and R - right).
2010-06-24 | E-GEOD-17524 | biostudies-arrayexpress
Project description:Although radiation effects have been extensively studied, the biological effects of low-dose radiation (LDR) are controversial. This study investigates LDR-induced alterations in locomotive behavior and gene expression profiles of Drosophila melanogaster. We measured locomotive behavior using larval pupation height and rapid iterative negative geotaxis (RING) assay after exposure to 0.1 Gy gamma-radiation (dose rate of 16.7 mGy/h). We also observed chronic LDR effects on development (pupation and eclosion rates) and longevity (life span). To identify chronic LDR effects on gene expression, we performed whole-genome expression analysis using gene-expression microarrays, and confirmed the results using quantitative real-time PCR. Pupation height was significantly higher after LDR treatment at the first larval instar. Locomotive behavior of male flies was significantly greater approximately 3M-BM--5 weeks after LDR, but pupation and eclosion rates and life spans were not significantly different. Genome-wide expression analysis identified 344 genes that were differentially expressed in irradiated larvae compared with those of controls. We identified several genes belonging to larval behavior functional groups such as locomotive behavior and oxidation reduction, and genes involved in conventional functional groups modulated by irradiation such as defense response, sensory and perception. Four candidate genes were confirmed as differentially expressed genes in irradiated larvae using qRT-PCR. These data suggest that LDR stimulates locomotion-related genes, and these genes can be used as potential markers for LDR. Eggs were collected from 5-day-old female flies and cultivated for 24 h on standard medium. Then, twenty larvae were manually selected and seeded on fresh standard medium in a new vial. After transfer, the experimental group of first-instar larvae was immediately irradiated with chronic gamma-radiation at a dose rate of 16.7 mGy/h. After treatment, gamma-irradiated flies and non-irradiated control flies were maintained in the same incubator at 25degC.
2014-09-26 | E-GEOD-61759 | biostudies-arrayexpress
Project description:We used microarray analysis to screen the Drosophila genome for effects of Wolbachia infection on transcript levels in wildtype adult immature ovaries. Keywords: Comparative expression analysis of infection effect To generate the ovaries to be compared, we first rid a wildtype Canton-S line of Drosophila of the well characterized YW strain of Wolbachia that it harbored (Bourtzis et al., 1998, Presgraves, 2000) by raising the flies for three generations on food containing tetracycline. After the line had been raised for three more generations on food without tetracycline, we used a standard PCR assay (O'Neil et al., 1999) to confirm that the line was Wolbachia free. Genetically matched infected and uninfected females were recovered as the daughters from two reciprocal crosses between the infected and the cured Canton-S lines. Previtellogenic ovaries were harvested from these females 1-5 h after eclosion
2010-05-14 | E-GEOD-9274 | biostudies-arrayexpress
Project description:Tumor hypoxia affects the aggressiveness and therapy response in solid tumors, including HPV-positive cancers. Cycling hypoxia, characterized by recurrent fluctuations in oxygen supply, is a prevalent, but much less investigated form of tumor hypoxia, and has been associated with a particularly therapy-resistant cancer cell subpopulation. Using mass spectrometry-based quantitative proteome analyses, we compare SiHa cells cultivated under normoxia (21% O2), physoxia (5.5% O2), chronic hypoxia (1% O2) and cycH (repeated cycles of 1 h at 1% O2 and 1 h at 5.5% O2) and assess distinct effects of cycH on the phenotype of HPV-positive cervical cancer cells.
2023-12-07 | PXD044908 | Pride