Insect gut metagenome
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ABSTRACT:
PROVIDER: PRJDB11190 | ENA |
REPOSITORIES: ENA
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Project description:Drosophila gut transcriptome in larvae and adult flies which experienced larval IMD activation
| PRJDB11191 | ENA
Project description:Activation of innate immune responses in the Drosophila larval fat body affects the physiological host responses. In order to characterize the effect of the activated immune responses in the fat body on the Drosophila, we used whole-genome microarray analysis and found that activation of the immune deficieny pathway (Imd) in the fat body alters the transcriptional profiles of Drosophila larvae. As we expected many of genes involved in regulation of antimicrobial peptides were upregulated in the larvae with elevated Imd activity in the fat body. Notably, we found activatioan of Imd in the fat body negatively affects expression of genes involved in glycolysis, energy production and insulin signaling pathway. Overall, our analysis showed that activation of innate immune signaling in the larval fat body significantly affects cellular pathways that regulate metabolism.
2018-01-24 | GSE109470 | GEO
Project description:The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection.
2007-07-07 | E-GEOD-2828 | biostudies-arrayexpress
Project description:The response of drosophila to bacterial and fungal infections involves two signaling pathways, Toll and Imd, which both activate NF-kB family members. We have studied the global transcriptional response of flies to infection with drosophila C virus. Viral infection induced a set of genes distinct from those regulated by the Toll or Imd pathways, and triggered activation of a STAT binding activity. Genetic experiments showed that the JAK kinase Hopscotch was involved in the control of the viral load in infected flies, and was required, though not sufficient, for the induction of some virus-regulated genes. Our results indicate that in addition to Toll and Imd, a third evolutionary conserved innate immunity pathway operates in drosophila and counters viral infection. Keywords: JAK/STAT virus drosophila immunity
2005-08-08 | GSE2828 | GEO
Project description:Plants can cope with stress better if they experience a mild form of the stress before the actual \\"real\\" stress event. In Arabidopsis thaliana it is known that plants that harboured eggs of the White cabbage butterfly (Pieris brassicae) before larval feeding can defend better against the herbivore stress. The main aim of the experiment was to compare the priming effect induced by insect egg deposition of Pieris brassicae between vegetative and reproductive (first open flowers) Arabidopsis thaliana plants on the transcriptional level. We used a full factorial setup consisting of a) untreated control plants , b) plants which experienced eggs for 6 days without larval feeding after that period, c) plants which experienced no eggs before larval feeding for 24 hours d) plants which experienced eggs for 6 days and larval herbivory for 24 hours. This setup was conducted with 6 week old vegetative plants and 10 week old reproductive plants were the first flowers were open. For all treatments leaf tissue from the leaves that experienced egg oviposition and/or larval feeding were collected. From reproductive plants flower buds were collected as well.
2022-05-10 | E-MTAB-9196 | biostudies-arrayexpress
Project description:We analysed the RNA-seq profile of larval and adult trachea of the fruitfly Drosophila melanogaster, as well as from whole flies.
2024-02-12 | GSE225000 | GEO
Project description:This project aims to define, by using a functional proteomic approach, the molecular partners associated with the canonical coupound of the IMD pathway. The Drosophila defense against pathogens largely relies on the activation of two major pathways, IMD and TOLL. The IMD pathway is activated mainly by Gram-negative bacteria, whereas the TOLL pathway responds predominantly to Gram-positive bacteria and fungi. The activation of this pathway leads to the rapid induction via NF-kB of numerous genes of the immune system, including various antimicrobial peptide genes. Recent evidence indicates that the IMD pathway is also involved in various other reactions in the absence of infection ("inflammatory-like" reactions). To gain a better understanding of the molecular machineries underlying the pleiotropic functions of this pathway, we have developed a proteomics analysis. Our first aim was to identify the proteins interacting with the 11 canonical members (PGRP-LC, PGRP-LE, IMD, BG4 (dFADD), DREDD, TAK1, TAB2, IAP2, IRD5 (DmIKKbeta), KEY (DmIKKgamma), and RELISH) previously shown to be involved in the activation of the IMD pathway. Each protein was fused N-terminally or C-terminally with a biotin tag and was stably expressed in S2 cells previously subjected to stable integration of the bacterial enzyme BirA to allow for biotinylation of the tags. In total, we established 22 stable transformant cell lines (11 genes x 2 tag locations), which were individually stimulated by heat-killed E.coli before harvest at 4 different time points (t=0 min, 10 min, 2 hour, and 8 hour). This procedure was followed by streptavidin-mediated affinity purification of 96 bait-protein complexes (22 transformants x 4 time points, plus 8 unstimulated controls without baits), on-bead trypsin digestions of the protein complexes and six LC-MS/MS analyses. We have identified 371 interactanting proteins in heat-killed E.coli stimulated Drosophila S2 cells, 90% of which have human orthologues. Comparative analysis of Gene Ontology (GO) annotation datasets from Human and Flies point to three significant common categories: (1) NuA4 Histone acetyltransferase complex, (2) SWI/SNF-type Chromatin remodeling complex, and (3) Transcription cofactor binding. Our Drosophila data point in particular to SUMOylation of the IkB-kinase homologue Ird5 in Drosophila, a level of regulation not described to date. Among numerous directions opened by our proteomics analysis, we have decided to first investigate this facet of the IMD pathway. We show nthat a highly conserved SUMOylation consensus site binds Drosophila SUMO (SMT3) in a challenge-dependent manner and that this process confers an increased level of activation of the antimicrobial peptide genes during bacterial challenge both in vitro and in flies. Our results demonstrate that SUMOylation of IKKbeta plays an important role in the induction of antimicrobial peptide genes. The MS analysis was performed on a FT ICR mass spectrometer (LTQ-FT Ultra, ThermoFisher Scientific, San Jose, CA) with the top 7 acquisition method: MS resolution 60,000, mass range 500-2000 Th, followed by 7 MS/MS (LTQ) on the 7 most intense peaks, with a dynamic exclusion for 90 s. The raw data were processed using Xcalibur 2.0.7 software. Each sample was first analyzed in triplicate then an exclusion list was added for three next runs. The database search was done on merged data using Mascot search engine (Matrix Science Mascot 2.3) on the 17D melanogaster databank (16535 sequences). Proteome Discoverer 1.3 (ThermoFisher Scientific) and Mascot were used to search the data and filter the results. The following parameters were used: up to 2 miss cleavages; MS tolerance 10 ppm; MSMS tolerance 1 Da; full tryptic peptides; partial modifications carbamidomethyla- tion (C), oxydation (M, H, W), Phosphorylation (Y).
2013-05-22 | PXD000129 | Pride
Project description:Alphaviruses establish a persistent infection in arthropod vectors, which is essential for effective transmission of the virus to vertebrate hosts. The development of persistence in insects is not well understood, although it is thought to involve the innate immune response. Using a transgenic fly system (SINrep) expressing a self-replicating viral genome, we have previously demonstrated the antiviral response of the Drosophila Imd (Immune Deficiency) and Jak-STAT innate immunity pathways. In the current study, microarray analysis of SINrep flies in comparison to control GFP flies aims to detect genes that are sensitive to Sindbis viral RNA replication. Both SINrep and GFP adult flies were harvested 3 days post eclosion for RNA extraction and hybridization on Affymetrix microarrays. We look for genes significantly altered in the presence of viral RNA replication.
2013-01-31 | E-GEOD-42726 | biostudies-arrayexpress
Project description:This study examined the transcriptomic response of Drosophila melanogaster larvae to crowding conditions. The phenotypic and transcriptomic changes from low larval density (5 eggs/ml) to medium density (60 eggs/ml) were minor, yielding somewhat reduced adult fitness and only 24 differentially expressed genes (DEGs). In contrast, high density (300 eggs/ml) caused extensive detrimental effects on adult fitness and yielded 2107 DEGs. Among these, upregulated gene sets were enriched in sugar, steroid and amino acid metabolism as well as DNA replication pathways, whereas downregulated gene sets were enriched in ABC transporters, Taurine, Toll/Imd signalling and P450 xenobiotics metabolism pathways.
2022-01-08 | GSE193120 | GEO
Project description:Viral infection in Drosophila triggers inducible gene expression, but the function of many of these genes and the biological significance of their induction remain poorly understood. Here, we report the functional characterization of the gene Diedel, which is strongly induced following some viral infections and encodes a 12kDa circulating protein. Diedel mutant flies have reduced viability and succumb rapidly to infection with Sindbis virus. This phenotype is associated with deregulated expression of IMD target genes and is rescued by mutations in the genes imd or IKKg, indicating that Diedel functions as an immunosuppressor cytokine targeting the IMD pathway. Homologues of Diedel are found in the genome of several DNA viruses, providing the first example of virokines in insects. Our results reveal that, besides RNA interference and apoptosis, an NF-kB pathway of inducible defense exerts evolutionary pressure on insect viruses. For each experimental condition (non infected and SINV infected), two biologically independent samples composed of 45 males of w1118 or Diedelcfm null mutant flies were used. Infection has been performed by injecting viral stocks prepared in Tris solution. Flies were then incubated for days at 29°C.
2016-01-07 | E-GEOD-68174 | biostudies-arrayexpress