Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1135339 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29816274_1.fastq.gz | Fastqsanger.gz | |||
| SRR29816274_2.fastq.gz | Fastqsanger.gz | |||
| SRR29816275_1.fastq.gz | Fastqsanger.gz | |||
| SRR29816275_2.fastq.gz | Fastqsanger.gz | |||
| SRR29816276_1.fastq.gz | Fastqsanger.gz |
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Project description:The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycetes-caused diseases such as Pythium myriotylum-caused rhizome rot in ginger leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using N. benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass content. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones, and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stress and the mechanisms of action of P. oligandrum as a biocontrol agent.
2023-06-22 | GSE235182 | GEO
Project description:Alternations in gene methylation and other epigenetic changes regulate normal development as well as drive disease progression. Chronic cigarette smoking causes hyper- and hypo-methylation of genes that could contribute to smoking-related diseases. It is unclear whether consumers of non-combustible tobacco, such as moist snuff, also exhibit such perturbations in their methylome. Here, we present global methylation changes relative to non-tobacco consumers in buccal cells collected from smokers (SMK) and moist snuff consumers (MSC). Generally healthy adult male study subjects were recruited into SMK, MSC and Non-Tobacco Consumer (NTC) cohorts (40 subjects/cohort). Global methylation profiling was performed on the Illumina 450K methylation array using buccal cell DNA. A total of 1,252 loci were found to be significantly differentially methylated in tobacco consumers relative to non-tobacco consumers. Overall, the SMK cohort exhibited larger qualitative and quantitative changes relative to MSC. Approximately half of the total number of gene loci, classified as Combustible Tobacco-Related signatures, and a third of the changes, termed Tobacco-Related signatures, were commonly detected in the tobacco consumers. Very few differences were detected between MSC and NTC, and hierarchical clustering of the top 50 significant gene loci suggested that MSC and NTC co-cluster. Consistent with physiological functions of AhR, combustible tobacco drives profound changes in buccal cell methylation status, principally impacting cell development and immune response pathways. These results aid in placing combustible and non-combustible tobacco products along a risk continuum and provide additional insights into the effects of tobacco consumption.
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Project description:The free-living soil fungus Trichoderma hamatum GD12 is notable amongst other Trichoderma strains in exhibiting both biocontrol and plant growth promotion (PGP) activities, which are coincident with a markedly expanded genome when compared to other characterised biocontrol and PGP isolates. Here, we make direct comparisons of T. hamatum GD12 transcription during PGP, and during antagonism of the root-infecting pathogen Sclerotinia sclerotiorum, in peat-based microcosms. An extensive mRNA-seq analysis sampling six time-points, 1, 2, 4, 7, 10 and 15 days after microcosm establishment revealed dynamic and biphasic signatures in the transcriptional responses of T. hamatum GD12 during Sclerotinia biocontrol and lettuce growth promotion. Functional analysis of differentially expressed genes demonstrated up-regulation of transportation and oxidation-reduction genes during both processes. Sclerotinia biocontrol is most likely mediated by the synthesis and secretion of antifungal compounds. Notably, the biphasic response during biocontrol was further characterised by the expression of a number of uncharacterised GD12 genes, small-secreted cysteine rich proteins and secondary metabolite producing gene clusters. This work demonstrates that T. hamatum GD12 harnesses a reservoir of uncharacterised genes that are actively engaged during effective biological control of a plurivorous plant pathogen.
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Project description:Tobacco use is an independent adverse prognostic feature in human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC). Despite this, the biologic features associated with tobacco use have not been systematically investigated in this population. We sought to characterize the genomic and immunologic features of HPV(+) OPSCC associated with tobacco use and adverse oncologic outcomes. Whole exome sequencing of 47 primary HPV(+) OPSCC tumors was performed to investigate mutational differences associated with tobacco exposure. To characterize the tumor immune microenvironment (TIME), targeted mRNA hybridization was performed. Low expression of transcripts in a T cell-inflamed gene expression profile (TGEP) was associated with tobacco use at the time of diagnosis and lower overall and disease-free survival. Tobacco use was associated with an increased proportion of T>C substitutions and a lower proportion of mutational signatures typically observed in HPV(+) OPSCC tumors, but was not associated with increases in mutational burden or the rate of recurrent oncogenic mutations. Our work suggests that rather than increased mutational burden, tobacco’s primary and clinically relevant association in HPV(+) OPSCC is immunosuppression of the tumor immune microenvironment.
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Project description:Transcriptional changes occurring at the infection site of 2 weeks old Cabernet sauvignon grapevine cuttings infected with a wood pathogen (Phaeomoniella chlamydospora) in the presence of a root-inoculated biocontrol agent (Pythium oligandrum). Gene expression profiling was done using the Nimblegen whole genome array with 3 biological replicates of 3 pooled wood chunks harvested 0 and 14 d after treatment (pathogen infection, biocontrol agent inoculation, mock treatment).
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