Drosophila melanogaster breed:yw, CanS, OrR
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ABSTRACT:
PROVIDER: PRJNA312721 | ENA |
REPOSITORIES: ENA
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Project description:To understand the effects of the microbiome of Drosophila melanogaster on host gene expression, we compared the transcriptome of guts from conventionally reared flies to their axenically (germ-free)-reared counterparts. Our analysis used dissected intestines from 4-7 day-old adult females and included two wild-type fly lines, OregonR and CantonS, as well as an immune-deficient line, RelishE20. With one of the wild-type lines, CantonS, we also looked at the impact of microbiome on the transcriptional profile of dissected intestines from aged cohorts (35-40 day-old females) and young (4-7 day-old) non-gut tissues (all tissues remaining from samples dissected for the analysis of guts.
2014-05-01 | E-MTAB-2447 | biostudies-arrayexpress
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:In animals studied to date, the crucial process of egg activation, by which an arrested mature oocyte transits into an actively developing embryo, initiates with an increase of Ca2+ in the oocyte’s cytoplasm. This Ca2+ rise sets off a series of downstream events, including the completion of meiosis and the dynamic remodeling of the oocyte transcriptome and proteome, which prepare the oocyte to undertake embryogenesis. Calcineurin is a highly conserved phosphatase that is activated directly by Ca2+ upon egg activation and that is required for the resumption of meiosis in Xenopus, ascidians and Drosophila. The molecular mechanisms by which calcineurin transduces the calcium signal to regulate meiosis and other downstream events are still unclear. In this study, we investigate the regulatory role of calcineurin during egg activation in Drosophila melanogaster. Using mass spectrometry, we quantify the phosphoproteomic and proteomic changes that occur during egg activation, and we examine how these events are affected when calcineurin function is perturbed in female germ cells. Our results show that calcineurin regulates hundreds of phosphosites and also influences the abundance of numerous proteins during egg activation. We find calcineurin-dependent changes in cell cycle regulators including Fzy, Greatwall (Gwl) and Endosulfine (Endos), protein translation modulators including PNG, NAT, eIF4G and eIF4B, and important components of signaling pathways including GSK3β and Akt1. Our results help elucidate the events that occur during the transition from oocyte to embryo
2019-03-13 | PXD011930 | Pride
Project description:In animals studied to date, the crucial process of egg activation, by which an arrested mature oocyte transits into an actively developing embryo, initiates with an increase of Ca2+ in the oocyte’s cytoplasm. This Ca2+ rise sets off a series of downstream events, including the completion of meiosis and the dynamic remodeling of the oocyte transcriptome and proteome, which prepare the oocyte to undertake embryogenesis. Calcineurin is a highly conserved phosphatase that is activated directly by Ca2+ upon egg activation and that is required for the resumption of meiosis in Xenopus, ascidians and Drosophila. The molecular mechanisms by which calcineurin transduces the calcium signal to regulate meiosis and other downstream events are still unclear. In this study, we investigate the regulatory role of calcineurin during egg activation in Drosophila melanogaster. Using mass spectrometry, we quantify the phosphoproteomic and proteomic changes that occur during egg activation, and we examine how these events are affected when calcineurin function is perturbed in female germ cells. Our results show that calcineurin regulates hundreds of phosphosites and also influences the abundance of numerous proteins during egg activation. We find calcineurin-dependent changes in cell cycle regulators including Fzy, Greatwall (Gwl) and Endosulfine (Endos), protein translation modulators including PNG, NAT, eIF4G and eIF4B, and important components of signaling pathways including GSK3β and Akt1. Our results help elucidate the events that occur during the transition from oocyte to embryo.
2018-11-29 | PXD010991 | Pride
Project description:metabolomics data for duodenum samples of germ free (GF) vs specific pathogen free (SPF) mice
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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:Transcriptomes of Drosophila melanogaster eye-antennal imaginal discs at three sequential larval stages: late 2nd instar (72h after egg laying (AEL)), mid 3rd instar (96h AEL) and late 3rd instar (120h AEL).
2018-01-08 | GSE94915 | GEO
Project description:Stable isotope labeling by amino acids in cell culture (SILAC) is widely used to quantify protein abundance in tissue culture cells. Until now, the only multicellular organism completely labeled at the amino acid level was the laboratory mouse. The fruit fly Drosophila melanogaster is one of the most widely used small animal models in biology. Here, we show that feeding flies with SILAC-labeled yeast leads to almost complete labeling in the first filial generation. We used these "SILAC flies" to investigate sexual dimorphism of protein abundance in D. melanogaster. Quantitative proteome comparison of adult male and female flies revealed distinct biological processes specific for each sex. Using a tudor mutant that is defective for germ cell generation allowed us to differentiate between sex-specific protein expression in the germ line and somatic tissue. We identified many proteins with known sex-specific expression bias. In addition, several new proteins with a potential role in sexual dimorphism were identified. Collectively, our data show that the SILAC fly can be used to accurately quantify protein abundance in vivo. The approach is simple, fast, and cost-effective, making SILAC flies an attractive model system for the emerging field of in vivo quantitative proteomics.
2015-10-12 | PXD003040 | Pride
Project description:Transcriptional profiling of anterior ovarioles (germaria and round previtellogenic egg chambers) of w1118 virgin females of Drosophila melanogaster 1 to 8 days post eclosion.
2016-04-04 | GSE79550 | 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