Ontology highlight
ABSTRACT:
PROVIDER: PRJNA949359 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23987500_1.fastq.gz | Fastqsanger.gz | |||
| SRR23987500_2.fastq.gz | Fastqsanger.gz | |||
| SRR23987501_1.fastq.gz | Fastqsanger.gz | |||
| SRR23987501_2.fastq.gz | Fastqsanger.gz | |||
| SRR23987502_1.fastq.gz | Fastqsanger.gz |
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Project description:An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface. A microarray was designed with probes for vertebrate-infecting virus sequences in EMBL, 18S rRNA fungi and parasite sequences from EMBL, and 16S rRNA sequences of bacteria from RDP, synthesized on the Agilent platform. The array was tested using 2 color dyes on cultured microbes and on clinical samples from sick and healthy people, looking for differences in clinically ill people compared to a number of healthy "controls".
2013-07-01 | E-GEOD-45860 | biostudies-arrayexpress
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Project description:Metaproteomic analysis of air particulate matter provides information about the properties of bioaerosols in the atmosphere and their influence on climate and public health. In this work, a new method for the extraction and analysis of proteins in airborne particulate matter from quartz microfiber filters was developed. Different protein extraction procedures were tested in order to select the best extraction protocol in terms of protein recovery. The optimized method was tested for extraction of proteins from spores of ubiquitous bacteria species and used for the first time for the metaproteomics characterization of filters from work environment. In particular, ambient aerosol samples were collected in different working environments, i.e. a composting plant, wastewater treatment plant and agricultural holding. One-hundred seventy-nine, 15, 205 and 444 proteins were successfully identified in composting plant, wastewater treatment plant, and agricultural holding, respectively. All identified proteins were mainly originate from fungi, bacteria and plants which is in line with the major categories of primary biological aerosol particles. The paper is the first metaproteomic study applied to bioaereosol samples collected in occupationally relevant environmental sites providing interesting information on the composting, wastewater treatment and feed blending processes. Significance This manuscript describes the metaproteomic analysis of aerosol samples collected in work enviroments. This is a novel use of aereosol samples and is needed as there is no really comprehensive way of analysing aereosol samples from a metaproteomic point of view. This paper could help to advance methods for metaproteomic analysis of bioaersols, specifically by comparing protein extraction protocols and pairing the best performing extraction protocol with a gel-free protein separation procedure applied for the first time for analysis of bioaerosol samples. The obtained data showed as bioaerosol was essentially made of fungi, bacteria and plant proteins, many of which could be associated to possible aerosolisation and could be a major health concern for workers on site and to the populations residing in neighbouring area.
2025-07-14 | PXD012345 | Pride
Project description:Endophytic fungi are fungi that live inside the roots of plants. They can promote plant growth through a variety of direct and indirect mechanisms. Direct mechanisms include the production of phytohormones, such as auxin and gibberellins, which can stimulate plant growth. Endophytic fungi can also fix nitrogen, solubilize phosphate, and produce siderophores, which are compounds that chelate iron and make it available to plants. In addition, some endophytic fungi produce antimicrobial metabolites that can protect plants from pests and pathogens. Indirect mechanisms include the induction of systemic resistance, which is a plant's ability to defend itself against pests and pathogens. Endophytic fungi can also help plants to tolerate abiotic stresses, such as drought, salinity, and heavy metals. In this study, we used a proteomic approach to identify the proteins that are expressed in rice plants after they are treated with endophytic fungi. We found that the treatment with endophytic fungi resulted in the expression of a number of proteins involved in plant growth, stress response, and defense. These results suggest that endophytic fungi can promote plant growth and improve plant resilience to stress.
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Project description:Background: Pectin is an abundant component in many fruit and vegetable wastes and could therefore be an excellent resource for biorefinery, but is currently underutilized. Fungal pectinases already play a crucial role for industrial purposes, such as for foodstuff processing. However, the regulation of pectinase gene expression is still poorly understood. For an optimal utilization of plant biomass for biorefinery and biofuel production, a detailed analysis of the underlying regulatory mechanisms is warranted. In this study, we applied the genetic resources of the filamentous ascomycete species Neurospora crassa to screen for transcription factors that play a major role in pectinase induction. Results: The pectin degradation regulator-1 (PDR-1) was identified through a transcription factor mutant screen in N. crassa. The Δpdr-1 mutant exhibited a severe growth defect on pectin and all tested pectin-related poly- and monosaccharides. Biochemical as well as transcriptional analyses of WT and the Δpdr-1 mutant revealed that while PDR-1-mediated gene induction was dependent on the presence of L-rhamnose, it also strongly affected the degradation of the homogalacturonan backbone. The expression of the endo-polygalacturonase gh28-1 was greatly reduced in the Δpdr-1 mutant, while the expression levels of all pectate lyase genes increased. Moreover, a pdr-1 overexpression strain displayed substantially increased pectinase production. Promoter analysis of the PDR-1 regulon allowed refinement of the putative PDR-1 DNA binding motif. Conclusions: PDR-1 is highly conserved in filamentous ascomycete fungi and is present in many pathogenic and industrially important fungi. Our data demonstrate that the function of PDR-1 in N. crassa combines features of two recently described transcription factors in Aspergillus niger (RhaR) and Botrytis cinerea (GaaR). The results presented in this study contribute to a broader understanding of how pectin degradation is orchestrated in filamentous fungi and how it could be manipulated for optimized pectinase production. The data here are associated with the following BioProjects: PRJNA256749, PRJNA349646, PRJNA349647, PRJNA349695, PRJNA349696, PRJNA349697, PRJNA349547, PRJNA349548, PRJNA349549, PRJNA349698, PRJNA349699, PRJNA349700 See the links on GSM entries for access to raw data at SRA.
2017-05-19 | GSE88985 | GEO
Project description:Thermally dimorphic human fungal pathogens undergo a reversible program of cellular differentiation in response to their environment that is essential for infectivity and pathogenicity. In the soil, these organisms grow as highly polarized, multicellular hyphal filaments that produce infectious particles. When inhaled by a mammalian host, these cells switch to a unicellular yeast form that causes disease even in healthy hosts. Temperature is considered to be the primary environmental cue that promotes reversible cellular differentiation; however, a shift to a lower temperature in vitro induces filamentous growth in an inefficient and asynchronous manner. In a search for other signals that regulate morphogenesis, we considered the monosaccharide N-acetylglucosamine (GlcNAc), which is a major component of microbial cell walls and is ubiquitous in the environment. GlcNAc was a potent and specific inducer of the yeast-to-filament transition in two thermally dimorphic fungi, Histoplasma capsulatum and Blastomyces dermatitidis. Micromolar concentrations of GlcNAc induced a robust morphological transition of H. capsulatum after temperature shift, indicating that fungal cells sense GlcNAc to promote filamentation. The synchronous morphologic transition stimulated by low temperature and GlcNAc allowed us to examine the temporal regulation of the transcriptome during morphogenesis to reveal candidate genes involved in establishing the filamentous growth program. Through this analysis, we identified two genes encoding GlcNAc transporters, NGT1 and NGT2, that were necessary for H. capsulatum cells to robustly filament in response to GlcNAc. Unexpectedly, NGT1 and NGT2 were important for efficient H. capsulatum yeast-to-filament conversion in standard glucose medium, suggesting that Ngt1 and Ngt2 monitor endogenous levels of GlcNAc to control multicellular filamentous growth in response to temperature. Overall, our work indicates that GlcNAc functions as a highly conserved cue of morphogenesis in fungi, which further enhances the significance of this ubiquitous sugar in cellular signaling in eukaryotes. For each time-course sample, cDNA was coupled to Cy5 and a reference cDNA pool was made by combining RNA from t = 0 and all late time course samples, which was coupled to Cy3. For end point microarray experiments (i.e., established yeast samples compared to established filamentous samples), G217B yeast cDNA was coupled to Cy5 and filament cDNA was coupled to Cy3.
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