Transcriptomic analysis of Aspergillus flavus in response to the solvent Dimethyl Sulfoxide
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA781981 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR16989239_1.fastq.gz | Fastqsanger.gz | |||
| SRR16989239_2.fastq.gz | Fastqsanger.gz | |||
| SRR16989240_1.fastq.gz | Fastqsanger.gz | |||
| SRR16989240_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 35 |
Similar Datasets
Project description:Dimethyl sulfoxide (DSMO) is a simple molecule widely used because of its great solvating ability. Beyond its physico-chemical properties, it is also biologically active, including on fungal species. Aspergillus flavus is a saprophytic and famous pathogenic fungus able to produce Aflatoxin B1 (AFB1), a potent carcinogenic mycotoxin which may contaminate many food crops. The aim of this study was to characterize the effect of DMSO on A. flavus transcriptome profile using high-throughput RNA-sequencing assay.
2021-12-20 | GSE189211 | GEO
Project description:Dimethyl sulfoxide (DMSO) is widely used as a solvent for water-insoluble substances and has biological properties such as inducing cellular differentiation, scavenging free radicals, and acting as a radioprotectant. DMSO has also been reported to enhance mineralization in osteoblastic cells. However, its molecular mechanisms have not yet been fully elucidated. In this study, we identified the differentially expressed genes associated with dimethyl sulfoxide-enhanced mineralization in mouse MC3T3-E1 preosteoblast cells using GeneChip® oligonucleotide microarrays.
2024-08-12 | GSE274013 | GEO
Project description:Current aquatic chemical testing guidelines recognise that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of sub-apical and chronic endpoints in future test strategies, however, suggests the limits may need re-assessment. To address this concern, microarrays were used to determine the effects of organic solvents, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO), upon the transcriptome of zebrafish (Danio rerio) embryos. Embryos were exposed for 48 h to 0.025 and 0.1 ml/L DMF or DMSO. Effects on survival and development after 24 and 48 h were assessed microscopically with no effects on mortality or morphology. However, analysis of 48-h embryonic RNA revealed large numbers of differentially expressed genes for both solvent at both concentrations. The enrichment of differentially expressed genes was found for metabolic, development and other key biological processes, some of which could be linked to observed morphological effects at higher solvent concentrations. These findings emphasise the need to remove or lower as far as possible, the concentrations of solvent carriers in ecotoxicology tests.
2011-10-06 | GSE32593 | GEO
Project description:The expression levels of uropathogenic E. coli (UPEC) UTI89 cells in YESCA broth with and without 4% dimehtyl sulfoxide (DMSO) and 2% ethanol (EtOH) were studied. To determine the up- or down-regulated expression profile in the presence of dimethyl sulfoxide (DMSO) and ethanol (EtOH), UPEC UTI89 were grown in YESCA broth with 4% dimethyl sulfoxide (DMSO) or 2% ethanol (EtOH) or no comound at 26°C with 200 rpm shaking for 24 hours were used for RNA extraction and hybridization on Affymetrix microarrays.
2012-02-15 | E-GEOD-35797 | biostudies-arrayexpress
Project description:Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and A. parasiticus. In order to better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. A. flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B1 and B2 biosynthesis, while A. parasiticus cultures had significantly increased B1 and G1 biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed seventy seven genes that are expressed significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis. Keywords: Aflatoxin, Aspergillus, flavus, Amnio Acids, Tryptophan
2007-06-07 | GSE6182 | GEO
Project description:Dimethyl sulfoxide (DSMO) is a simple molecule widely used because of its great solvating ability, but this solvent also has little-known biological effects, especially on fungi. Aspergillus flavus is a notorious pathogenic fungus which may contaminate a large variety of crops worldwide by producing aflatoxins, endangering at the same time food safety and international trade. The aim of this study was to characterize the effect of DMSO on A. flavus including developmental parameters such as germination and sporulation, as well as its transcriptome profile using high-throughput RNA-sequencing assay and its impact on secondary metabolism (SM). After DMSO exposure, A. flavus displayed depigmented conidia in a dose-dependent manner. The four-day exposition of cultures to two doses of DMSO, chosen on the basis of depigmentation intensity (35 mM "low" and 282 mM "high"), led to no significant impact on fungal growth, germination or sporulation. However, transcriptomic data analysis showed that 4891 genes were differentially regulated in response to DMSO (46% of studied transcripts). A total of 4650 genes were specifically regulated in response to the highest dose of DMSO, while only 19 genes were modulated upon exposure to the lowest dose. Secondary metabolites clusters genes were widely affected by the DMSO, with 91% of clusters impacted at the highest dose. Among these, aflatoxins, cyclopiazonic acid and ustiloxin B clusters were totally under-expressed. The genes belonging to the AFB1 cluster were the most negatively modulated ones, the two doses leading to 63% and 100% inhibition of the AFB1 production, respectively. The SM analysis also showed the disappearance of ustiloxin B and a 10-fold reduction of cyclopiazonic acid level when A. flavus was treated by the higher DMSO dose. In conclusion, the present study showed that DMSO impacted widely A. flavus' transcriptome, including secondary metabolism gene clusters with the aflatoxins at the head of down-regulated ones. The solvent also inhibits conidial pigmentation, which could illustrate common regulatory mechanisms between aflatoxins and fungal pigment pathways. Because of its effect on major metabolites synthesis, DMSO should not be used as solvent especially in studies testing anti-aflatoxinogenic compounds.
| S-EPMC8703953 | biostudies-literature
Project description:Current aquatic chemical testing guidelines recognise that solvents can potentially interfere with the organism or environmental conditions of aquatic ecotoxicity tests and therefore recommend concentration limits for their use. These recommendations are based on evidence of adverse solvent effects in apical level tests. The growing importance of sub-apical and chronic endpoints in future test strategies, however, suggests the limits may need re-assessment. To address this concern, microarrays were used to determine the effects of organic solvents, dimethylformamide (DMF) and dimethyl sulfoxide (DMSO), upon the transcriptome of zebrafish (Danio rerio) embryos. Embryos were exposed for 48 h to 0.025 and 0.1 ml/L DMF or DMSO. Effects on survival and development after 24 and 48 h were assessed microscopically with no effects on mortality or morphology. However, analysis of 48-h embryonic RNA revealed large numbers of differentially expressed genes for both solvent at both concentrations. The enrichment of differentially expressed genes was found for metabolic, development and other key biological processes, some of which could be linked to observed morphological effects at higher solvent concentrations. These findings emphasise the need to remove or lower as far as possible, the concentrations of solvent carriers in ecotoxicology tests. Balanced loop design consisting of five separate conditions - two exposure concentrations for each of the two solvents and a control treatment - using four replicates for each condition all of which were dye swapped, resulting in a total of twenty independant samples on twenty arrays.
2011-10-05 | E-GEOD-32593 | biostudies-arrayexpress
Project description:RNA-seq was used to compare differential gene expressions for Aspergillus flavus wild type strain and ASPES transcription factor deletion strains.The goals of this study are to explore the aflatoxin regulation pathway in A. flavus.
2018-12-25 | GSE107025 | GEO
Project description:Aspergillus flavus and A. parasiticus are two of the most important aflatoxin-producing species that contaminate agricultural commodities worldwide. Both species are heterothallic and undergo sexual reproduction in laboratory crosses. Here, we examine the possibility of interspecific matings between A. flavus and A. parasiticus. These species can be distinguished morphologically and genetically, as well as by their mycotoxin profiles. Aspergillus flavus produces both B aflatoxins and cyclopiazonic acid (CPA), B aflatoxins or CPA alone, or neither mycotoxin; Aspergillus parasiticus produces B and G aflatoxins or the aflatoxin precursor O-methylsterigmatocystin, but not CPA. Only four out of forty-five attempted interspecific crosses between compatible mating types of A. flavus and A. parasiticus were fertile and produced viable ascospores. Single ascospore strains from each cross were isolated and were shown to be recombinant hybrids using multilocus genotyping and array comparative genome hybridization. Conidia of parents and their hybrid progeny were haploid and predominantly monokaryons and dikaryons based on flow cytometry. Multilocus phylogenetic inference showed that experimental hybrid progeny were grouped with naturally occurring A. flavus L strain and A. parasiticus. Higher total aflatoxin concentrations in some F1 progeny strains compared to midpoint parent aflatoxin levels indicate synergism in aflatoxin production; moreover, three progeny strains synthesized G aflatoxins that were not produced by the parents, and there was evidence of putative allopolyploidization in one strain. These results suggest that hybridization is an important diversifying force resulting in the genesis of novel toxin profiles in these agriculturally important species.
2015-10-01 | GSE61981 | GEO
Project description:Objective: Aspergillus flavus aflR, a gene encoding a Zn(II)2Cys6 DNA-binding domain, is an important transcriptional regulator of the aflatoxin biosynthesis gene cluster. Our previous results of GO analysis for the binding sites of AflR in A. flavus suggest that AflR may play an integrative regulatory role. This study aimed to investigate the integrative function of the aflR gene in A. flavus. Design: In this study, we used Aspergillus flavus NRRL3357 as a wild-type strain (WT) and constructed a knockout strain of A. flavus ΔaflR by homologous recombination. Based on the transcriptomics technology, we investigated the metabolic effects of aflR gene on growth, development and toxin synthesis of A. flavus, and discussed the overall regulation mechanism of aflR gene on A. flavus at the transcriptional level. Results: The disruption of aflR severely affected the aflatoxin biosynthetic pathway, resulting in a significant decrease in aflatoxin production. In addition, disrupted strains of the aflR gene produced relatively sparse conidia and a very small number of sclerotia. However, the biosynthesis of cyclopiazonic acid (CPA) was not affected by aflR gene disruption. Transcriptomic analysis of the ΔaflR strain grown on potato dextrose agar (PDA) plates at 0 h, 24 h, and 72 h showed that expression of clustering genes involved in the biosynthesis of aflatoxin was significantly down-regulated. Meanwhile, the ΔaflR strain showed significant expression differences in genes involved in spore germination, sclerotial development, and carbohydrate metabolism compared to the WT strain. Conclusions: The results showed that the A. flavus aflR gene also played a positive role in the growth and development of fungi.
2021-07-16 | GSE179978 | GEO