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E-MTAB-2740

ABSTRACT: Transcription profiling by array of intestinal tissue from Drosophila w1118 and p38c null mutation flies

PROVIDER: E-MTAB-2740 | ExpressionAtlas | 2015-07-13

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-2740-analysis-methods.tsv	Tabular
	E-MTAB-2740-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-2740-configuration.xml	Xml
	E-MTAB-2740-percentile-ranks.tsv	Tabular
	E-MTAB-2740.condensed-sdrf.tsv	Tabular

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Heterozygous mutation of NF-B innate immune response transcription factor Relish increases survival following traumatic brain injury in Drosophila

Project description:Traumatic brain injury (TBI) pathologies are caused by primary and secondary injuries. Primary injuries result from physical damage to the brain, and secondary injuries arise from cellular responses to primary injuries. A characteristic cellular response is sustained activation of inflammatory pathways commonly mediated by NF-B transcription factors. Using a Drosophila melanogaster TBI model, we previously found that the main proximal transcriptional response to primary injuries is triggered by activation of Toll and Imd innate immune response pathways that engage NF-B factors Dif and Relish (Rel), respectively. Here, we monitor the abundance of Rel protein by mass spectrometry (MS) and observe that Rel increases in fly heads at 4-8 h after TBI. To investigate the necessity of Rel for secondary injuries, we generated a null allele, Reldel, by CRISPR/Cas9 editing. Heterozygous but not homozygous Reldel mutation reduced mortality at 24 h after TBI and increased the lifespan of injured flies. Additionally, the effect of heterozygous Reldel mutation on mortality was modulated by genetic background and diet. To identify genes that facilitate effects of heterozygous Reldel mutation on TBI outcomes, we compared genome-wide mRNA expression profiles of uninjured and injured +/+, +/Reldel, and Reldel/Reldel flies at 4 h following TBI. Only a few genes changed expression more than two-fold in +/Reldel flies relative to +/+ and Reldel/Reldel flies, and they were not canonical innate immune response genes. Therefore, Rel is necessary for TBI-induced secondary injuries but in complex ways involving Rel gene dose, genetic background, diet, and possibly small changes in expression of innate immune response genes.

2020-12-04 | PXD021869 | Pride

Revisiting the role of beta-tubulin in Drosophila development: beta-tubulin60D is not an essential gene, and its novel Pin1 allele has a tissue-specific dominant-negative impact

Project description:Diversity in cytoskeleton organization and function may be achieved through alternative tubulin isotypes and by a variety of post-translational modifications. The Drosophila genome contains five different β-tubulin paralogs, which may play an isotype tissue-specific function in vivo. One of these genes, the beta-tubulin60D gene, which is expressed in a tissue-specific manner, was found to be essential for fly viability and fertility. To further understand the role of the beta-tubulin60D gene, we generated new beta-tubulin60D null alleles (beta-tubulin60DM) using the CRISPR/Cas9 system and found that the homozygous flies were viable and fertile. Moreover, using a combination of genetic complementation tests, rescue experiments, and cell biology analyses, we identified Pin1, an unknown dominant mutant with bristle developmental defects, as a dominant-negative allele of beta-tubulin60D. We also found a missense mutation in the Pin1 mutant that results in an amino acid replacement from the highly conserved glutamate at position 75 to lysine (E75K). Analyzing the β-tubulin structure suggests that this E75K alteration destabilizes the alpha-helix structure and may also alter the GTP-Mg2+ complex binding capabilities. Our results revisited the credence that beta-tubulin60D is required for fly viability and revealed for the first time in Drosophila, a novel dominant-negative function of missense beta-tubulin60D mutation in bristle morphogenesis

2022-02-17 | PXD030317 | Pride

Indirect Flight Muscle (IFM) expression profiling of actin and myosin nulls in Drosophila melanogaster

Project description:Expression profiling of IFMs from 1-2 day old adult male flies of 3 genotypes: Canton-S, IFM-specific actin null (Act88FKM88) and IFM-specific myosin null (Mhc7). Results provide insight into how muscles respond to the absence of major scaffold proteins, and whether these transcriptional responses are filament-specific or generic to the tissue. RNA was extracted from the IFMs of 1-2 day old adult male flies of 3 genotypes (Canton-S, Act88FKM88, Mhc7), labeled, and hybridized on Affymetrix GeneChip Drosophila Genome 2.0 microarrays. 9 microarray experiments from 3 independent biological replicates of each genotype. Data was analyzed using RMA method, and significance was tested using SAM version 3.02, with cut-off parameters of 10% FDR and minimum 2-fold change in expression levels.

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Peroxisome elevation induces stem cell differentiation and intestinal epithelial repair

Project description:To identify the regulators that directly interact with peroxisomes to promote the differentiation of intestinal stem and progenitor cells after injury, peroxisomes were isolated from both wild-type and Pex10-null flies and mass spectrometry (MS) analysis was performed. For peroxisomes isolation and mass spectrometry, 100 female 5-day-old wild-type or Pex10-null files without bleomycin treatment (BLM-0D WT, BLM-0D Pex10-null) or treatment with bleomycin for one day followed by recovery for one day (BLM-REC-1D WT, BLM-REC-1D Pex10-null) were homogenized. Each group repeat two times. The MS analysis was performed on Q ExactiveTM Mass Spectrometer (Thermo). The peptides were subjected to NSI source followed by tandem mass spectrometry (MS/MS) in Q ExactiveTM Mass Spectrometer coupled online to the HPLC. Intact peptides were detected in the Orbitrap at a resolution of 70,000 and peptides were selected for MS/MS using NCE setting as 27. Protein identification was performed with MASCOT software by searching Uniprot Drosophila melanogaster.

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Indirect Flight Muscle (IFM) expression profiling of actin and myosin nulls in Drosophila melanogaster

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Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish

Project description:To identify genes regulated by Relish in both the absence and presence of TBI in Drosophila, we compared genome-wide mRNA expression of control flies, as well as flies that were heterozygous or homozygous for a null allele of relish with and without injury.

2020-08-29 | GSE157102 | GEO

Profiling of gene expression during aging in isolated bodies of wild type vs Cdk5a-mutant Drosophila melanogaster.

Project description:To provide a consistent background for studies of the link between neurodegeneration and aging, we performed microarray-based expression profiling (Affymetrix) of RNA isolated from the bodies of adult Drosophila at various ages from either wild type flies (Oregon R), or flies bearing a null mutation of the gene encoding the Cdk5 activator (Cdk5a). Note that all flies were wild type for the chromosomal white locus due to the pleiotropic effects of the w locus on many neuronal and physiological functions of the adult fly. In order to match samples by ‘physiological age’ in the two populations, WT flies were collected at 10 days, 20 days, 41 days and 58 days after eclosion and Cdk5a flies were collected at 10, 23, and 31 days (NOTE: 41 days for WT and 23 days for Cdk5a corresponded to <10% population mortality; 58 days (WT) and 31 days (Cdk5a) corresponded to ~50% population mortality in this experiment). These samples provide a well-matched basis for identification of genes with age-dependent expression level in each of the two genotypes and for comparison of differences in expression between the genotypes.

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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.

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Project description:The role of RNA silencing as a defense mechanism against viruses remains to be formerly established in mammalian somatic cells. Here, we determined the antiviral properties of human and Drosophila Dicer proteins in a heterologous setup. We expressed human Dicer (hDicer) in Drosophila, and Drosophila Dicer-2 in human cells, and measured the impact on the response to Sindbis virus (SINV) infection. In flies, hDicer presents a low processing activity, but partially rescues a Dcr2 null mutation in flies. Expression of Dicer-2 in HEK293 cells allows the processing of SINV RNA into 21-nt-long small RNAs. Nevertheless, instead of conferring a protective effect against SINV, Dicer-2 expression increases viral replication in HEK293 cells. We present evidence that this effect is due to a competition with the interferon pathway. Our results therefore suggest that adding functionial RNA silencing machinery in IFN-competent differentiated mammalian cells can be detrimental for antiviral defense.

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