Ontology highlight
ABSTRACT:
PROVIDER: PRJNA758737 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Aim of this project is to identify biomarkers associated with fungal persistence in the host and genomic variability among strains isolated from different environments.
2016-04-30 | E-SYBR-8 | biostudies-arrayexpress
Project description:Eosinophilia is associated with various persisting inflammatory diseases and often coincides with chronic fungal infections or fungal allergy as in case of allergic bronchopulmonary aspergillosis (ABPA). However, the interactions between eosinophils and fungal pathogen leading to release of inflammatory mediators from eosinophils are poorly understood. Therefore, we established a co-culture system of mouse bone marrow derived eosinophils (BMDE) with Aspergillus fumigatus (Af) that we used in part to analyse transcriptional regulation induced by Af.
2022-05-31 | GSE165694 | GEO
Project description:Severe, early-onset photoreceptor (PR) degeneration associated with MERTK mutations is thought to result from failed phagocytosis by retinal pigment epithelium (RPE). Notwithstanding, the severity and onset of PR degeneration in mouse models of Mertk ablation is determined by the hypomorphic expression or the loss of the Mertk paralog Tyro3. Here we find that loss of Mertk and reduced expression/loss of Tyro3 led to RPE inflammation, even before eye-opening. Incipient RPE inflammation cascaded to involve microglia activation and PR degeneration with monocyte infiltration. Inhibition of RPE inflammation with the JAK1/2 inhibitor ruxolitinib mitigated PR degeneration in Mertk -/- mice. Neither inflammation nor severe, early-onset PR degeneration were observed in mice with defective phagocytosis alone. Thus, inflammation drives severe, early-onset PR degeneration-associated with Mertk loss of function.
2023-01-20 | GSE214005 | GEO
Project description:The adaptation of fungal pathogens to the host environment via large-scale genomic changes is a poorly characterized phenomenon. We recently discovered clinical strains of Cryptococcus neoformans, the leading cause of fungal meningoencephalitis in HIV/AIDS patients, which are disomic for chromosome 13. In the current study, we examined the relationship between disomy, expression of the virulence factor melanin and virulence in a mouse model of cryptococcosis. We found that melanin production was correlated with monosomy at chromosome 13, and that disomic variants were less melanized and attenuated for virulence in mice. Changes in the copy number of other chromosomes were also detected in strains showing variation in melanin formation after growth in culture and after passage through mice. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebral spinal fluid of AIDS patients and minimally cultured provided evidence for mixed infections and copy number variation. Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Importantly, genome variation is associated with virulence factor expression and disease severity, and its occurrence in isolates from AIDS patients suggests that it may have clinical relevance.
2011-05-31 | GSE29627 | GEO
Project description:The adaptation of fungal pathogens to the host environment via large-scale genomic changes is a poorly characterized phenomenon. We recently discovered clinical strains of Cryptococcus neoformans, the leading cause of fungal meningoencephalitis in HIV/AIDS patients, which are disomic for chromosome 13. In the current study, we examined the relationship between disomy, expression of the virulence factor melanin and virulence in a mouse model of cryptococcosis. We found that melanin production was correlated with monosomy at chromosome 13, and that disomic variants were less melanized and attenuated for virulence in mice. Changes in the copy number of other chromosomes were also detected in strains showing variation in melanin formation after growth in culture and after passage through mice. A survey of environmental and clinical isolates maintained in culture revealed few occurrences of disomic chromosomes. However, an examination of isolates that were freshly collected from the cerebral spinal fluid of AIDS patients and minimally cultured provided evidence for mixed infections and copy number variation. Overall, these results suggest that the genome of C. neoformans exhibits a greater degree of plasticity than previously appreciated. Importantly, genome variation is associated with virulence factor expression and disease severity, and its occurrence in isolates from AIDS patients suggests that it may have clinical relevance.
2011-06-01 | GSE29671 | GEO
Project description:Retinal degeneration is the leading cause of irreversible blindness. Retinitis pigmentosa (RP) is a genetically heterogenous group of diseases. In the United States, approximately one in 4000 individuals is affected. RP begins with the loss of night vision due to the loss of rod photoreceptor cells. The disease progresses slowly with the loss of peripheral vision, and eventually leads to complete debilitating and irreversible blindness. The first mutation associated with human RP was identified in the gene encoding rhodopsin, the G-protein coupled receptor of rod photoreceptor cells. Mutations within the rhodopsin gene account for significant portion of RP cases. Specifically, mutations of the proline at residue 347 in rhodopsin have been linked to human RP. We are fortunate to have access to the P347S rhodopsin mutant mice. These mice represent an excellent transgenic mouse model of retinal degeneration. The P347S rhodopsin mutation is one of the best studied mutations, yet the mechanism by which the mutation causes degeneration is still unknown. One study has demonstrated that galectin-1 plays a role in degeneration of neuronal processes (1) and another study has shown that expression level of galectin-3 is elevated in retinas of patients with age-related macular degeneration. These studies in conjunction with the availibility of the P347S mutant mice have provided impetus to examine the pathogenesis of retinal degeneration in the context of the possible role of glycans and glycan-binding proteins. The time course of photoreceptor degeneration in the P347S mouse model has been carefully studied. In these mice, degeneration is barely detectable at 1 month of age, yet biochemical evidence suggests that the rod photoreceptor cells have already begun to die. At 4 months of age, approximately half of the rod photoreceptor cells have degenerated. To distinguish involvement of glycogens at the various stages of retinal degeneration, we have collected retinas of wild type and the mutant mice at four time points (1, 2, 3, and 4 months of age). This will allow us to identify the genes that target early, mid- and late stages of the retinal degeneration process. Thus we request the analysis of total 24 samples as specified below: Age Group (months) Mice No of samples at each time point 1 Wild type 3 2 Wild type 3 3 Wild type 3 4 Wild type 3 1 P347S 3 2 P347S 3 3 P347S 3 4 P347S 3 Total 24.
2011-09-07 | E-GEOD-31990 | biostudies-arrayexpress
Project description:Cockayne syndrome is an inherited premature aging syndrome associated with developmental and neurological disorders. Mutations in the genomic locus encoding CSB are associated with 80% Cockayne syndrome cases. CSB is invovled in relieving UV-induced and oxidative stree. To gain more insights into the fucntion of CSB under these stress, we use ChIP-seq to determine the genomic localization of CSB 1 hour after UV irradiation and menadione treatment. Genomic localization of CSB and remodeling deficient CSBâN1
2015-11-09 | E-GEOD-50925 | biostudies-arrayexpress
Project description:11 Mycobacterium tuberculosis mutants resistant to D-cycloserine were isolated in the laboratory. Genomic DNA was isolated and whole genomes were sequenced to perform SNP calling and identify possible mutations associated with resistance.
2018-12-28 | E-MTAB-5935 | biostudies-arrayexpress
Project description:Retinitis Pigmentosa is a group of inherited eye disorders characterized by progressive degeneration of photoreceptor cells in the retina, leading to vision loss and eventual blindness. One of the known genetic mutations associated with RP is the c.6926A>C mutation in the RPE (retinal pigment epithelium) cells. The dataset involves multiple experimental approaches and cell types, providing a comprehensive understanding of the disease and potential corrective strategies.
2024-03-13 | E-MTAB-13171 | biostudies-arrayexpress
Project description:Recurrent gene mutations, chromosomal translocations, acquired genomic copy number aberrations (aCNA) and copy-neutral loss-of-heterozygosity (cnLOH) underlie the genomic pathogenesis of acute myelogenous leukemia (AML). Genomic lesion types from all of these categories have been variously associated with AML patient outcome. However, the patterns of co-occurrence of such lesions are only now beginning to be defined, and we seek to further delineate the relative influence of different types of genomic alterations on clinical outcomes in AML. In this study, we performed SNP 6.0 array-based genomic profiling of aCNA/cnLOH along with sequence analysis of 13 recurrently mutated genes on purified leukemic blast DNA from 156 prospectively enrolled non-FAB-M3 AML patients across the clinical spectrum of de novo, secondary, and therapy-related AML. We identify positive and negative associations of gene mutations, specific aCNA/cnLOH or total aCNA/cnLOH counts with different AML types as well as the associations of specific mutations with overall genomic complexity or genomic stability. Further, we show that NPM1, RUNX1, ASXL1 and TP53 mutations, elevated SNP-A-based genomic complexity, and specific recurrent aCNAs predict response to induction chemotherapy. Finally, results of comprehensive multivariate analyses support a dominant role for TP53 mutations or elevated genomic complexity as predictors of short survival in AML. Integrated genomic profiling of a clinically relevant adult AML population reveals the interplay between gene mutations, recurrent aCNAs, and SNP-A-based genomic complexity and identifies among them the genomic characteristics most associated with types of response to intensive induction therapies and with shortened overall survival.
2015-03-01 | GSE61323 | GEO