Flu infection
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA215372 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12494412_1.fastq.gz | Fastqsanger.gz | |||
| SRR12494412_2.fastq.gz | Fastqsanger.gz | |||
| SRR12494425_1.fastq.gz | Fastqsanger.gz | |||
| SRR12494425_2.fastq.gz | Fastqsanger.gz | |||
| SRR953151.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Shortly after the release of singlet oxygen (1O2), drastic changes in nuclear gene expression occur in the conditional flu mutant of Arabidopsis that reveal a rapid transfer of signals from the plastid to the nucleus. In contrast to retrograde control of nuclear gene expression by plastid signals described earlier, the primary effect of 1O2 generation in the flu mutant is not the control of chloroplast biogenesis but the activation of a broad range of signaling pathways known to be involved in biotic and abiotic stress responses. This activity of a plastid-derived signal suggests a new function of the chloroplast, namely that of a sensor of environmental changes that activates a broad range of stress responses. Inactivation of the plastid protein EXECUTER1 attenuates the extent of 1O2-induced up-regulation of nuclear gene expression, but it does not fully eliminate these changes. A second related nuclear-encoded protein, dubbed EXECUTER2, has been identified that is also implicated with the signaling of 1O2-dependent nuclear gene expression changes. Like EXECUTER1, EXECUTER2 is confined to the plastid. Inactivation of both EXECUTER proteins in the ex1/ex2/flu triple mutant is sufficient to suppress the up-regulation of almost all 1O2-responsive genes. Retrograde control of 1O2-responsive genes requires the concerted action of both EXECUTER proteins within the plastid compartment. Experiment Overall Design: Two individual biologica replicates, each containing material of five mature plants of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, respectively, were used for the microarray analysis. Plants were germinated on soil and kept under continuous light until the beginning of bolting and then transferred to the dark for 8 h. Dark-incubated mature plants were reilluminated for 30 min and subsequently harvested for RNA extraction. Experiment Overall Design: The EX1 (At4g33630) T-DNA insertion line SALK 002088 and EX2 (At1g27510) T-DNA insertion line SALK 012127 were obtained from the European Arabidopsis Stock Centre (NASC). Homozygous mutant lines were identified by PCR analysis by using T-DNA-, EX1- and EX2-specific primers. Both T-DNA-lines were crossed with a flu Col-0 line that had been obtained by 5 backcrosses of flu1-1 in Landsberg erecta with wild-type Columbia. The ex1/flu and ex2/flu mutant lines were crossed, and within the segregating F2 population triple mutants were identified by PCR-based genotyping. For the cultivation of mature plants, seeds of wild type, flu, ex1/flu, ex2/flu, and ex1/ex2/flu, all in Col-0 ecotype, were sown on soil and plants were grown under continuous light (100 mol m 2 s 1).
2008-04-08 | E-GEOD-10509 | biostudies-arrayexpress
Project description:Effect of various dark incubation times on gene expression in Arabidopsis flu mutant
2021-02-28 | GSE111284 | GEO
Project description:Older adults have diminished immune responses that increase susceptibility to infectious diseases, such as influenza (flu). In older adults, flu infection can lead to hospitalization, catastrophic disability, and mortality. We previously demonstrated severe and prolonged muscle degradation and atrophy in aged mice during flu infection. Here, we utilized an unbiased transcriptomic analysis to elucidate mechanisms of flu-induced muscular declines in a mouse model. Our results showed age-related gene expression differences including downregulation of genes associated with muscle regeneration and organization and upregulation of genes associated with pro-inflammatory cytokines and migratory immune pathways in aged mice when compared to young. Pathway analysis revealed significant enrichment of leukocyte migration and T cell activation pathways in the aged muscle during infection. Intramuscular CD4 T cells increased in both young and aged mice during infection, while intramuscular CD8 T cells increased exclusively in aged muscle. CD4 T cells in young muscle were regulatory T cells (Treg), while those in aged were T follicular helper (Tfh) and Th2 cells. Correspondingly, IL-33, an important cytokine for Treg accumulation within tissue, increased only in young flu-infected muscle. Conversely, CXCL10 (IP-10) increased only in aged muscle suggesting a continued recruitment of CD8 T cells into the aged muscle during flu infection. Overall, our findings elucidate a link between flu-induced disability and dysregulated intracellular T cell recruitment into flu-injured muscle with aging. Furthermore, we uncovered potential pathways involved that can be targeted to develop preventative and therapeutic interventions to avert disability and maintain independence following infection.
2023-09-05 | GSE241965 | GEO
Project description:The investigators overall goals are to adapt, implement, evaluate, and disseminate the FLU-FOBT Program as an integrated nurse-run, primary care-based intervention that can reduce colorectal cancer screening disparities in resource-poor clinical settings. In this program, fecal occult blood tests (FOBT) are provided with influenza vaccinations (FLU) to eligible patients between the ages of 50 and 75 during FLU season. The investigators hypothesis is that the FLU-FOBT Program can be adapted for primary care settings and lead to higher rates of colorectal cancer screening (CRCS).
| 2095822 | ecrin-mdr-crc
Project description:This project investigates the serum proteomic signatures of the serological response to flu vaccination. We profiled the serum proteome of 160 flu vaccine recipients from a cohort study conducted in 2019-2020 season, with DIA-MS based proteomics. We compared the protein level between low and high responders based on the response measure seroconversion, as well as the adjusted seroconversion which excludes the confoudning effects of all the semographic factors recorded for these participants. We did the analysis for the composite seroconversion as well as for the individual strains. We also investigated the complex impact of age.
2022-11-17 | PXD036718 | Pride
Project description:The goal of this study was to examine differential gene expression in human platelets, focusing on it's relationship to flu vaccine response and how it may vary with age.
2023-05-31 | GSE178158 | GEO
Project description:We used the flu mutant of Arabidopsis and a transgenic line that overexpresses the thylakoid-bound ascorbate peroxidase (tAPX) to address the interactions between different reactive oxygen species (ROS) signaling pathways. The conditional flu mutant of Arabidopsis accumulates excess protochlorophyllide in the dark within chloroplast membranes that upon illumination acts as a photosensitizer and generates singlet oxygen (1O2). Immediately after the release of singlet oxygen rapid changes in nuclear gene expression occur. Distinct sets of genes were activated that were different from those induced by other reactive oxygen species, superoxide or hydrogen peroxide (H2O2), suggesting that different types of active oxygen species activate distinct signaling pathways. It was not known whether the pathways operate separately or interact with each other. We have addressed this problem by modulating noninvasively the level of H2O2 in plastids by means of a transgenic line that overexpresses the thylakoid-bound ascorbate peroxidase (tAPX, line 14/2 PMID: 15165186). In the flu mutant overexpressing tAPX, the expression of most of the nuclear genes that were rapidly activated after the release of 1O2 was significantly higher in flu plants overexpressing tAPX, whereas in wild-type plants, overexpression of tAPX had only a very minor impact on nuclear gene expression. The results suggest that H2O2 antagonizes the 1O2-mediated signaling of stress responses as seen in the flu mutant. This cross-talk between H2O2- and 1O2-dependent signaling pathways might contribute to the overall stability and robustness of wild-type plants exposed to adverse environmental stress conditions. Experiment Overall Design: Arabidopsis thaliana rosette leaves were harvested after 2 h of reillumination following a 8h dark period for RNA extraction and hybridization on Affymetrix ATH1 microarrays. The entire experiment was performed six times, providing independent biological replicates. For each of the six experiments, all four lines, wild-type, thylakoidal ascorbate peroxidase overexpressor (over tAPX, line 14/2), flu mutant and flu plants overexpressing thylakoidal ascorbate peroxidase were grown for 3 weeks under continuous light at 90 mmol. m-2 . s-1, transferred to the dark for 8 h, and reilluminated for 120 min before the rosette leaves of at least 10 plants per line were harvested. Total RNAs from three separate biological experiments were pooled (= 1 biological rep.) for the preparation of cDNA and the subsequent synthesis of biotin-labeled complementary RNA as recommended by Affymetrix.
2008-04-05 | E-GEOD-10812 | biostudies-arrayexpress
Project description:Epidemiological studies link NDDs with exposure to maternal viral infection in utero. As the immature brain is vulnerable to insult, it is thought that prenatal inflammation alters neurodevelopmental trajectories, leading to NDD pathologies. Using a biologically relevant mouse model of live influenza (flu) infection during pregnancy, we aim to determine if gestational flu infection triggers detrimental maternal cell signaling that leads to NDD-relevant pathologies in offspring. Overall, this work will improve translation to the clinic and will build a foundation for developing targeted therapeutics for NDDs that can be delivered during gestation.
2024-06-20 | GSE262291 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-03-03 | GSE49934 | GEO
Project description:Time course data from influenza A-infected mice were collected for up to 60 days after infection to monitor gene expression profiles of the host. Whole lungs of individual mice were harvested from three independent infection experiments and at least three biological replicates were taken for a single time point. Mock-infected mice served as controls. Early after infection, the activation of RIG-I and interferon pathways as well as the up-regulation of chemokine and cytokine expression revealed the innate immune response phase which was closely correlated with the presence of infectious virus. Subsequently, viral clearance was initiated by the onset of T cell infiltration. In the late phase of infection, the formation of tertiary lymphoid tissues, bronchus-associated lymphoid tissue (BALT), was observed. The formation of BALT resulted in permanent steady-state changes of the lung transcriptome.
2012-06-30 | E-MTAB-764 | biostudies-arrayexpress