Ontology highlight
ABSTRACT:
PROVIDER: PRJNA354793 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5049320.fastq.gz | Fastqsanger.gz | |||
| SRR5049330.fastq.gz | Fastqsanger.gz | |||
| SRR5049321.fastq.gz | Fastqsanger.gz | |||
| SRR5049331.fastq.gz | Fastqsanger.gz | |||
| SRR5049322.fastq.gz | Fastqsanger.gz |
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Project description:<p><em>Anisakis simplex</em> are parasitic nematodes that cause anisakiasis. The possibility of infection with this parasite is through consumption of raw or undercooked fish products. <em>A. simplex</em> infections are often misdiagnosed, especially in subclinical cases that do not present with typical symptoms such as urticaria, angioedema and gastrointestinal allergy. The resulting allergic reactions range from rapid-onset and potentially fatal anaphylactic reactions to chronic, debilitating conditions. While there have been numerous published studies on the genomes and proteomes of <em>A. simplex</em>, less attention has been paid to the metabolomes. Metabolomics is concerned with the composition of metabolites in biological systems. Dynamic responses to endogenous and exogenous stimuli are particularly well suited for the study of holistic metabolic responses. In addition, metabolomics can be used to determine metabolic activity at different stages of development or during growth. In this study, we reveal for the first time the metabolomes of infectious stages (L3 and L4) of <em>A. simplex</em> using untargeted metabolomics by ultra-performance liquid chromatography-mass spectrometry. In the negative ionization mode (ESI-), we identified 172 different compounds, whereas in the positive ionization mode (ESI+), 186 metabolites were found. Statistical analysis showed that 60 metabolites were found in the ESI- mode with different concentration in each group, of which 21 were more enriched in the L3 larvae and 39 in the L4 stage of <em>A. simplex</em>. Comparison of the individual developmental stages in the ESI+ mode also revealed a total of 60 differential metabolites, but 32 metabolites were more enriched in the L3 stage larvae, and 28 metabolites were more concentrated in the L4 stage. The metabolomics study revealed that the developmental stages of <em>A. simplex</em> differed in a number of metabolic pathways, including nicotinate and nicotinamide metabolism. In addition, molecules responsible for successful migration within their host, such as pyridoxine and prostaglandins (E1, E2, F1a) were present in the L4 stage. In contrast, metabolic pathways for amino acids, starch and sucrose were mainly activated in the L3 stage. Our results provide new insights into the comparative metabolome profiles of two different developmental stages of <em>A. simplex</em>.</p>
2023-07-08 | MTBLS6458 | MetaboLights
Project description:Plants are naturally associated with diverse microbial communities, which play significant roles in plant performance, such as growth promotion or fending off pathogens. The roots of Alkanna tinctoria L. are rich in naphthoquinones, particularly the medicinally used chiral compounds alkannin, shikonin and their derivatives. Former studies already have shown that microorganisms may modulate plant metabolism. To further investigate the potential interaction between A. tinctoria and associated microorganisms we performed a greenhouse experiment, in which A. tinctoria plants were grown in the presence of three distinct soil microbiomes. At four defined plant developmental stages we made an in-depth assessment of bacterial and fungal root-associated microbiomes as well as all primary and secondary metabolites. Our results showed that the plant developmental stage was the most important driver influencing the plant metabolite content, revealing peak contents of alkannin/shikonin at the fruiting stage. In contrast, the soil microbiome had the biggest impact on the plant root microbiome. Correlation analyses performed on the measured metabolite content and the abundance of individual bacterial and fungal taxa suggested a dynamic, at times positive or negative relationship between root-associated microorganisms and root metabolism. In particular, the bacterial Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group and the fungal species Penicillium jensenii were found to be positively correlated with higher content of alkannins.
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Project description:According to the European Food Safety Authority (EFSA), A. simplex has been classified as a biohazardous organism. Most developmental stages of parasitic nematodes occur under anaerobic conditions, and larvae obtain most of their energy from saccharides. The effect of glucose from the external environment has not been described in L3 and L4 larvae of A. simplex. Another advantage is that only these stages have been identified as pathogenic in humans. In this study, we aimed to uncover genes and pathways controlling glucose (10 mg/mL) action by an integrated analysis of the transcriptome and proteome of L3 and L4 larval stages of A. simplex. The proteome results yielded a total of 6,441 proteins that were filtered for further analysis. The final repository consists of 464 proteins, which were identified in a group as up-regulated DEPs, e.g., malate dehydrogenase, and down-regulated DEPs, e.g., methylmalonyl-CoA epimerase. The results obtained should lead to a better understanding of the molecular processes underlying the development of A. simplex infection in humans and will add to the existing knowledge on the role of nutrients of this parasite.
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Project description:Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of lodgepole pine (Pinus contorta) inoculated with the mountain pine beetle (Dendroctonus ponderosae) vectored fungal pathogen Grosmannia clavigera or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 2% of the lodgepole pine transcriptome.
2012-12-01 | GSE22924 | GEO
Project description:Using 21K spruce microarray (that contains 21.8 thousand unique transcripts) we performed analysis of the transcriptome response of lodgepole pine (Pinus contorta) inoculated with the mountain pine beetle (Dendroctonus ponderosae) vectored fungal pathogen Grosmannia clavigera or treated with wounding. This microarray analysis revealed large transcriptome reorganization with close to 2000 transcripts (10% of the studied transcriptome) differentially expressed within two weeks of treatment, with the wounding response affecting close to 2% of the lodgepole pine transcriptome. RNA was isolated from the bark of lodgepole pine inoculated with Grosmannia clavigera, treated with wounding, or untreated control for three time points (6h, 2days and 2 weeks). Three independent biological replicates were included for each treatment and each time point. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points (total 36 hybridizations/slides).
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