Fungal isolates
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA413482 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole genome sequencing of SYBARIS Aspergillus spp. known to be multi-drug resistant and difficult to treat. Aim of this experiment is to investigate the genetic basis of susceptibility to disease and elucidate molecular mechanisms of drug resistance in these strains.
2016-04-30 | E-SYBR-1 | biostudies-arrayexpress
Project description:Fungal isolate diversity and Bd-inhibition on Colorado boreal toads
| PRJEB46768 | ENA
Project description:Rhizoctonia solani Kühn is a soilborne basidiomycetous fungus that causes significant damage to many economically important crops. R. solani isolates are classified into 13 Anastomosis Groups (AGs) with interspecific subgroups having distinctive morphology, pathogenicity and wide host range. However, the genetic factors that drive the unique fungal pathology are still not well characterized due to the limited number of available annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 13 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT, AG3-TB, AG4-HG-I, AG5, AG6, and AG8). Here, we report a pangenome comparative analysis of 13 R. solani isolates covering important groups to elucidate unique and common attributes associated with each isolate, including molecular factors potentially involved in determining AG-specific host preference. Finally, we present the largest repertoire of annotated R. solani genomes, compiled as a comprehensive and user-friendly database, viz. RsolaniDB. Since 7 genomes are reported for the first time, the database stands as a valuable platform for formulating new hypotheses by hosting annotated genomes, with tools for functional enrichment, orthologs and sequence analysis, currently not available with other accessible state-of-the-art platforms hosting Rhizoctonia genome sequences.
2020-10-03 | E-MTAB-9588 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are small, stable non-coding RNA molecules with regulatory function and marked tissue specificity that post-transcriptionally regulate gene expression, however their role in fungal keratitis remain unknown. Our purpose was to identify the miRNAs in human cornea from fungal keratitis patients and understand their key role in regulation of pathogenesis. Corneal samples from normal cadaver (n=3) and fungal keratitis (n=5) patients were pooled separately and total RNA was extracted. Deep sequencing was done using Illumina HiSeq1000 platform to identify miRNA profile. We identified seventy five differentially expressed miRNAs in fungal keratitis corneas. Select miRNAs were validated by real-time RT-PCR (Q-PCR). We predicted their role in regulating target genes in several pathways by combining miRNA target genes and pathway analysis, and mRNA expression of select target genes were further analysed by Q-PCR. MiR-21-5p, miR-223-3p, miR-146b-5p, miR-155-5p, miR-511-5p were found to be involved in inflammatory and immune responses, regulating Toll like receptor signaling pathways, which is of particular interest. MiR-451a with an increased expression in keratitis may have a role in wound healing by targeting Macrophage Migration Inhibitory Factor (MIF). Further, we highlighted that Neurotrophin signaling pathway may play a role in wound healing process. One novel miRNA was also detected in cornea. In conclusion, several miRNAs with high expression in fungal keratitis corneas point towards their role in regulation of pathogenesis. Further insights in understanding miRNAs role in wound healing and inflammation may help design new therapeutic strategies.
2016-07-28 | GSE64843 | GEO
Project description:RATIONALE: Gathering information about how often fungal infections of the blood occur in patients with cancer or in patients who have undergone stem cell transplant may help doctors learn more about the disease.
PURPOSE: This natural history study is collecting information about fungal infections of the blood over time from patients with cancer or from patients who have undergone a stem cell transplant.
| 2037924 | ecrin-mdr-crc
Project description:Purpose: A common theme across multiple fungal pathogens is their ability to impair the establishment of a protective immune response. Although early inflammation is beneficial in containing the infection, an uncontrolled inflammatory response is detrimental and may eventually oppose disease eradication. Chromoblastomycosis (CBM), a cutaneous and subcutaneous mycosis, caused by dematiaceous fungi, is capable of inducing a chronic inflammatory response. This work was performed in order to understand how fungal cells were able to induce intense inflammatory response in the host. Methods:Peritoneal macrophages (PM) were infected for 6h with F. pedrosoi conidia or muriform cells and then lysed so that total RNA was extracted with the RNeasy kit (Qiagen). Paired-end cDNA reads (100bp) were generated using the HiSeq 2000 Sequencing system (Illumina) located at the Scripps DNA Sequencing Facility (California, USA). Quality check of the paired-end reads was performed using FASTQC, and clipping and trimming was done using CUTADAPT and PRINSEQ softwares, respectively. The filtered reads were aligned to the mouse genome downloaded from the Ensembl database using open source TopHat 2.0.9. The aligned files were ordered and indexed using Samtools followed by read count using HTSeq-count. Statistical analysis was done using the R environment for statistical computing. Gene model quantification were performed using the Bioconductor package EdgeR. Results: High throughput RNA sequencing analysis (RNA-Seq) showed a strong up-regulation of genes related to fungal recognition, cell migration, inflammation, apoptosis and phagocytosis in macrophages exposed in vitro to Fonsecaea pedrosoi muriform cells, but not F. pedrosoi conidia. This is the main fungal form responsible for the intense inflammatory pattern observed in CBM, clarifying the chronic inflammatory reaction observed in most patients. Conclusions: Our findings reveal two different fungal-host interaction strategies according to fungal form, highlighting fungal dimorphism as an important key in understanding the bipolar nature of inflammatory response in fungal infections
2017-05-01 | GSE84257 | GEO
Project description:Low coverage whole genome sequencing of samples from individuals from Friuli Venezia Giulia, an Italian genetic isolate population.
| EGAS00001000252 | EGA
Project description:Rhizophagus irregularis strain:several fungal isolates Targeted Locus (Loci)
| PRJNA213169 | ENA
Project description:Within the last decades, invasive fungal infections have gained increasing significance. They are characterized by high mortality rates and are often caused Candida albicans and Aspergillus fumigatus. The increasing number of infections underlines the necessity for additional anti-fungal therapies, which require an extended knowledge of gene regulations during fungal infection. MicroRNAs are regulators of important cellular processes, including immune response. By analyzing their regulation and impact on target genes, novel therapeutic approaches may be developed. Here, we examine the role of microRNAs in human dendritic cells during fungal infections. Dendritic cells represent the bridge between the innate and the adaptive immune systems. Therefore, analysis of gene regulation of dendritic cells is of particular significance. By applying next-generation sequencing of small RNAs, we quantify microRNA expression in monocyte-derived dendritic cells after 6 and 12h of infection with C. albicans and A. fumigatus as well as treatment with LPS. We use two different tools and an online database to determine potential target genes. We identified 29 microRNAs that are differentially regulated after infection by the fungi or LPS. Two and five of them are specific for fungal infections after 6h and 12h, respectively. We further validated interactions of miR-132-5p and miR-212-5p with immunological relevant target genes, such as FKBP1B, KLF4, and SPN, on both RNA and protein level. Our results indicate a fine-tuning function of these microRNAs during fungal infections. Beyond that, we identified previously undiscovered microRNAs. We validated three novel microRNAs via qRT-PCR. A comparison with known microRNAs revealed possible relations with the miR-378 family and miR-1260a/b for two of them, while the third one features a unique sequence with no resemblance to known microRNAs. In summary, this study analyzes the effect of known microRNAs in dendritic cells during fungal infections and proposes novel microRNAs that could be experimentally verified.
2017-06-12 | GSE80014 | GEO