Ontology highlight
ABSTRACT:
PROVIDER: PRJNA393046 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5802900.fastq.gz | Fastqsanger.gz | |||
| SRR5802901.fastq.gz | Fastqsanger.gz | |||
| SRR5802902.fastq.gz | Fastqsanger.gz | |||
| SRR5802903.fastq.gz | Fastqsanger.gz | |||
| SRR5802904.fastq.gz | Fastqsanger.gz |
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Project description:β-glucans, which can activate innate immune responses, are a major component in the cell wall of the cyst form of Pneumocystis. In the current study we examined whether β-1,3 glucans are masked by surface proteins in Pneumocystis, and what role β-glucans play in Pneumocystis-associated inflammation. For 3 species, including P. jirovecii, which causes Pneumocystis pneumonia (PCP) in humans, P. carinii, and P. murina, β-1,3 glucans were masked in most organisms, as demonstrated by increased exposure following trypsin treatment. Using Q-PCR and microarray techniques, we demonstrated in a mouse model of PCP that treatment with caspofungin, an inhibitor of β-1,3 glucan synthesis, for 21 days, decreased expression of a broad panel of inflammatory markers, including IFN-γ, TNF-α, IL-1β, IL-6, and multiple chemokines/chemokine ligands. Thus, β-glucans in Pneumocystis cysts are largely masked, which likely decreases innate immune activation; this mechanism presumably was developed for interactions with immunocompetent hosts, in whom organism loads are substantially lower. In immunosuppressed hosts with a high organism burden, organism death and release of glucans appears to be an important contributor to deleterious host inflammatory responses.
2016-08-31 | GSE79079 | GEO
Project description:The cell wall is a structure involved in important stages of fungal growth and morphogenesis. Several studies in the literature have shown how perturbations at the cell wall-level trigger dramatic effects on growth (e.g. Horiuchi, 2009). Despite the importance of fungal cell walls and despite the great advances made in the field, there are still missing pieces in our understanding of cell wall dynamics in filamentous fungi. Some cell wall biosynthetic genes, for example, are still uncharacterized (for a detailed inventory of Aspergillus nidulans cell wall-related genes, see de Groot et al., 2009). The chief polysaccharides in the cell wall of the model organism A. nidulans are β-glucans (β-1,3-, β-(1,3;1,4)- and β-1,6-glucans), chitin and α-1,3-glucans. While much is known about the chitin and α-1,3-glucan biosynthetic genes in A. nidulans (Horiuchi et al., 1999; Fujiwara et al., 2000; Ichinomiya et al., 2002 and 2005; Takeshita et al., 2006; Yoshimi et al., 2013), no characterization is yet available for the celA gene (ANIA_08444) encoding a putative mixed-linkage glucan synthase (de Groot et al., 2009). Recently, a study on A. fumigatus has characterized Tft1, an enzyme shown to be responsible for the production of β-(1,3;1,4)-glucans in this organism (Samar et al., 2015). Deletion of Tft1 causes no obvious phenotype in A. fumigatus and a modest increase in virulence. To characterize the role of β-(1,3;1,4)-glucans in the growth and development of filamentous fungi, we here sought to provide transcriptomics data of an A. nidulans strain showing reduced expression of the gene encoding the putative mixed linkage glucan synthase celA.
2017-07-26 | GSE94110 | GEO
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. Both cytosolic and plastidial isoforms of GAPDH has been described but the in vivo functions of the plastidial isoforms is unresolved. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2) and performed a microarray analysis comparing gapcp double (gapcp1 gapcp2) mutant and wild type seedlings Experiment Overall Design: 15-day old Arabidopsis seedlings (Col 0) and gapcp1gapcp2 double mutants were used for RNA extraction and hybridization on Affymetrix microarrays.
2009-02-21 | E-GEOD-14765 | biostudies-arrayexpress
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. Both cytosolic and plastidial isoforms of GAPDH has been described but the in vivo functions of the plastidial isoforms is unresolved. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2) and performed a microarray analysis comparing gapcp double (gapcp1 gapcp2) mutant and wild type seedlings
2009-02-10 | GSE14765 | GEO
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA. 15-day old Arabidopsis seedlings (Col 0) and gapcp1gapcp2 double mutants were used for RNA extraction and hybridization on Affymetrix microarrays.
2010-05-28 | E-GEOD-21765 | biostudies-arrayexpress
Project description:Glycolytic Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) catalyzes the conversion of glyceraldehyde 3-phospate to 1,3-bisphosphoglycerate by coupling with the reduction of NAD+ to NADH. We generated mutants of the Arabidopsis plastidial GAPDH isoforms (At1g79530, At1g16300; GAPCp1, GAPCp2). gapcp double mutants (gapcp1 gapcp2) display a drastic phenotype of arrested root development and sterility.Complex interactions occurring between ABA and sugar signal transduction pathways have been shown, but the molecular mechanisms connecting both pathways are not well understood. Since we found drastic carbohydrate changes in gapcp1 gapcp2, we studied their response to ABA. by performing a microarray analysis comparing gapcp1 gapcp2 and wild type seedlings after a long term treatment with ABA.
2010-05-11 | GSE21765 | GEO
Project description:This experiment focused on the transcriptomic responses of the rainbow trout spleen macrophage-like cell line (RTS11) in response to β-glucans (M-glucans, Biotec). RTS11 was cultured at the Scottish Fish Immunology Research Centre, University of Aberdeen. M-glucans was provided by Skretting AI. Samples were treated for 4hrs with either M-glucans or left untreated as controls (n=4). To establish responses to β-glucans, total RNA was extracted for RNA-seq examination. Library preparation and sequencing was carried out by Novogene Ltd, with downstream analysis being carried out at the SFIRC. As a result, a total of 8 samples were used to identify responses to M-glucans, 4 control and 4 stimulated samples were used for the analysis.
2023-03-31 | E-MTAB-12643 | biostudies-arrayexpress
Project description:Chitin oligomers, released from fungal cell walls by endochitinase, induce defense and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2,375 EST clones representing putative defense-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered >3-fold in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes are those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress expression of some genes. These data indicate that Arabidopsis will be an excellent model to elucidate mechanisms of chitin elicitation in plant defense.
2005-09-02 | E-SMDB-1627 | biostudies-arrayexpress
Project description:Chitin oligomers, released from fungal cell walls by endochitinase, induce defense and related cellular responses in many plants. However, little is known about chitin responses in the model plant Arabidopsis. We describe here a large scale characterization of gene expression patterns in Arabidopsis in response to chitin treatment using an Arabidopsis microarray consisting of 2,375 EST clones representing putative defense-related and regulatory genes. Transcript levels for 71 ESTs, representing 61 genes, were altered >3-fold in chitin-treated seedlings relative to control seedlings. A number of transcripts exhibited altered accumulation as early as 10 min after exposure to chitin, representing some of the earliest changes in gene expression observed in chitin-treated plants. Included among the 61 genes are those that have been reported to be elicited by various pathogen-related stimuli in other plants. Additional genes, including genes of unknown function, were also identified broadening our understanding of chitin-elicited responses. Among transcripts with enhanced accumulation, one cluster was enriched in genes with both the W-box promoter element and a novel regulatory element. In addition, a number of transcripts had decreased abundance, encoding several proteins involved in cell wall strengthening and wall deposition. The chalcone synthase promoter element was identified in the upstream regions of these genes, suggesting that pathogen signals may suppress expression of some genes. These data indicate that Arabidopsis will be an excellent model to elucidate mechanisms of chitin elicitation in plant defense. Groups of assays that are related as part of a time series. Keywords: time_series_design
2005-09-09 | GSE3273 | GEO