Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1061649 | ENA |
REPOSITORIES: ENA
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Project description:Naegleria gruberi is a single-celled eukaryote best known for its remarkable ability to form an entire microtubule cytoskeleton de novo during its metamorphosis from an amoeba into a flagellate, including two basal bodies (equivalent to centrioles), two flagella (equivalent to cilia), and a cytoplasmic microtubule array. This full-genome transcriptional analysis, performed at 20-minute intervals throughout Naegleria differentiation, reveals vast transcriptional changes, including the differential expression of cytoskeletal, metabolism, signaling and stress response genes. Naegleria gruberi (strain NEG) was grown in association with Kleibsiella pneumoniae on solid media. Cells were prepared and differentiated using standard protocols, and harvested at 0, 20, 40, 60 and 80 minutes after initiation of differentiation. Three independent biological replicates were obtained from differentiating N. gruberi. Each replicate series included the following timepoints: 0, 20, 40, 60 and 80 minutes after initiation of differentiation.
2010-09-02 | E-GEOD-21527 | biostudies-arrayexpress
Project description:Naegleria gruberi is a single-celled eukaryote best known for its remarkable ability to form an entire microtubule cytoskeleton de novo during its metamorphosis from an amoeba into a flagellate, including two basal bodies (equivalent to centrioles), two flagella (equivalent to cilia), and a cytoplasmic microtubule array. This full-genome transcriptional analysis, performed at 20-minute intervals throughout Naegleria differentiation, reveals vast transcriptional changes, including the differential expression of cytoskeletal, metabolism, signaling and stress response genes. Naegleria gruberi (strain NEG) was grown in association with Kleibsiella pneumoniae on solid media. Cells were prepared and differentiated using standard protocols, and harvested at 0, 20, 40, 60 and 80 minutes after initiation of differentiation.
2010-09-02 | GSE21527 | GEO
Project description:Transcriptome of Naegleria gruberi
| PRJEB23822 | ENA
Project description:Although copper is an essential nutrient crucial for many biological processes, an excessive concentration can be toxic and lead to cell death. The metabolism of this two-faced metal must be strictly regulated at the cell level. In this study, we investigated copper homeostasis in two related unicellular organisms: nonpathogenic Naegleria gruberi and the “brain-eating amoeba” Naegleria fowleri. We identified and confirmed the function of their specific copper transporters securing the main pathway of copper acquisition. Adjusting to different environments with varying copper levels during the life cycle of these organisms requires various metabolic adaptations. Using comparative proteomic analyses, measuring oxygen consumption, and enzymatic determination of NADH dehydrogenase, we showed that both amoebas respond to copper deprivation by upregulating the components of the branched electron transport chain: the alternative oxidase and alternative NADH dehydrogenase. Interestingly, analysis of iron acquisition indicated that this system is copper-dependent in N. gruberi but not in its pathogenic relative. Importantly, we identified a potential key protein of copper metabolism of N. gruberi, the homolog of human DJ-1 protein, which is known to be linked to Parkinson’s disease. Altogether, our study reveals the mechanisms underlying copper metabolism in the model amoeba N. gruberi and the fatal pathogen N. fowleri and highlights the differences between the two amoebas.
2022-05-20 | PXD032745 | Pride
Project description:Naegleria gruberi whole genome sequencing project
| PRJNA14010 | ENA
Project description:Expression analysis of Naegleria gruberi (strain NEG) during differentiation from the amoeba to the flagellate form
| PRJNA125955 | ENA
Project description:Naegleria gruberi strain:NEG-M | isolate:Schardinger | cultivar:ATCC30224 Genome sequencing and assembly
| PRJNA1019389 | ENA
Project description:During mitosis, RNA polymerase and most transcription factors are excluded from the chromosomes and transcription ceases. The transcriptional re-activation of the genome, following mitosis, requires the re-setting of cell-type specific programs that were initially established during development. However, only about one-fifth of transcription factors are retained on chromosomes throughout mitosis and a subset of these have been shown to facilitate target gene reactivation during mitotic exit. How such M-bM-^@M-^\bookmarkingM-bM-^@M-^] factors bind to chromatin in mitosis and re-activate transcription is central to the stability of transcriptional programs across multiple cell cycles. We compared a diverse set of transcription factors involved in liver differentiation and found different modes of mitotic chromosome binding. The pioneer transcription factor FoxA1, which is among the first to bind liver genes in development, exhibits virtually complete mitotic chromosome binding, whereas other liver factors bind with a range of efficiencies. Yet genome-wide analysis shows that only about 15% of the FoxA1 interphase target sites are bound in mitosis; the latter include sites at genes for maintaining cell differentiation. FoxA1 mutants that perturb specific and nonspecific DNA binding reveal a significant contribution of nonspecific binding events in mitotic chromatin. Such nonspecific binding appears to spread from interphase FoxA1 targets and may serve as storage sites. The hierarchy of specific binding, nonspecific binding, partial chromatin binding, and failure to bind mitotic chromosomes reflects the temporal sequence of the factorsM-bM-^@M-^Y developmental roles in gene activation. Three replicate chIP-seq data sets each are included for mitotic and asynchronously cycling cells; a single input lane from each condition is also included.
2013-03-31 | E-GEOD-39241 | biostudies-arrayexpress