Fungi
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ABSTRACT:
PROVIDER: PRJNA614507 | ENA |
REPOSITORIES: ENA
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Project description:Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The oligonucleotides selected for fungal identification and the oligonucleotides specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory and food samples offering an interesting potential for microbiological laboratories. Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins Development of a diagnostic array for the identification of food-borne fungi and their potential mycotoxin-producing genes. Oligonucleotide probes to be printed onto the array were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. Analysis was performed with 40 fungal cultures were obtained from the Agricultural Research Council culture collection (ARC), Pretoria, South Africa.an in-house spotted oligonucleotide microarray. The identity of each fungus was confirmed by standard laboratory procedures. For DNA isolation, the fungal strains were grown on 1.5% malt extract agar at 25°C for 1-2 weeks and total genomic fungal DNA was extracted following the DNA extraction protocol described by Raeder and Broda (1985). The internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4 were used as a reference for normalization of all spot intensity data.Samples were fluorescently labelled with Cy5 dye by using a Cyâ¢Dye Post-labelling Reactive Dye Pack and wre hybridized to the oligonucleotide microarray overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
2010-05-07 | E-GEOD-19227 | biostudies-arrayexpress
Project description:Nucleolar ribosomal DNA (rDNA) repeats control ribosome manufacturing. rDNA harbors a ribosomal RNA (rRNA) gene and an intergenic spacer (IGS). RNA polymerase (Pol) I transcribes rRNA genes yielding the rRNA components of ribosomes. Pol II at the IGS induces rRNA production by preventing Pol I from excessively synthesizing IGS non-coding RNAs (ncRNAs) that can disrupt nucleoli. At the IGS, Pol II regulatory processes and whether Pol I function can be beneficial remain unknown. Here, we identify IGS Pol II regulators, uncovering nucleolar optimization via IGS Pol I. Compartment-enriched proximity-dependent biotin identification (compBioID) showed enrichment of the TATA-less promoter-binding TBPL1 and transcription regulator PAF1 with IGS Pol II. TBPL1 localizes to TCT motifs, driving Pol II and Pol I and maintaining its baseline ncRNA levels. PAF1 promotes Pol II elongation, preventing unscheduled R-loops that hyper-restrain IGS Pol I and its ncRNAs. PAF1 or TBPL1 deficiency disrupts nucleolar organization and rRNA biogenesis. In PAF1-deficient cells, repressing unscheduled IGS R-loops rescues nucleolar organization and rRNA production. Depleting IGS Pol I-dependent ncRNAs is sufficient to compromise nucleoli. We present the interactome of nucleolar Pol II and show its control by TBPL1 and PAF1 ensures IGS Pol I ncRNAs maintaining nucleolar structure and operation.
2024-10-09 | GSE261857 | GEO
Project description:Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 alpha) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotide probes directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The probes selected for fungal identification and the probes specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify single pure strains or cultures of potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory samples and maize-derived foods offering an interesting potential for microbiological laboratories. Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins
2010-03-01 | GSE19227 | GEO
Project description:Heat shock-induced ribosomal intergenic spacer RNA
| PRJNA475962 | ENA
Project description:To identify potential single-guide RNA (sgRNAs) contaminants in the GMP HBG-sgRNA, we performed SMARTer smRNA-sequencing (Takara). 80.79% of the 5' spacer sequence perfectly matched the targeting sgRNA sequence and no evidence of contaminants sgRNAs that could target other genomic regions.
2024-08-21 | GSE275157 | GEO
Project description:Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing how Cre distinguishes between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. To fill this gap, we investigated target site variations of identical pairs of the loxP 8 bp spacer region, screening 6,000 unique loxP-like sequences. Approximately 84% of these sites exhibited efficient recombination, affirming the flexibility of spacer sequences for catalysis. However, certain spacers negatively impacted recombination, emphasizing sequence dependence. Directed evolution of Cre on inefficiently recombined spacers not only yielded recombinases with enhanced activity but also mutants with reprogrammed selective activity. Mutations altering spacer specificity were identified, and molecular modelling and dynamics simulations elucidated the mechanism behind this specificity switch. These findings highlight the potential to fine-tune site-specific recombinases for spacer sequence specificity, offering a novel concept to enhance the applied properties of designer-recombinases for genome engineering applications.
2024-07-25 | GSE254392 | GEO
Project description:In yeast, the phosphatase Cdc14 is required for mitotic exit and for segregation of repetitive regions. Cdc14 is also a subunit of the silencing complex RENT, but no roles in transcription repression have been described. Here we report that Cdc14 promotes silencing at the integenic spacer sequences (IGS) of ribosomal genes during interphase and at Y' repeats in sub-telomeric regions during mitosis, through its ability to dephosphotylate the CDT domain of the RNA polymerase II.
2011-07-29 | GSE31020 | GEO
Project description:Fungal Internal Transcribed Spacer RNA (ITS) RefSeq Targeted Loci Project
| PRJNA177353 | ENA
Project description:Bacterial promoters consist of core sequence motifs termed –35 and –10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on E. coli. However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N-terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of B. longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSS) of the B. longum NCC2705 strain were identified using RNA-Seq analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the –35 and –10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed thirty-seven plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the –35 and –10 boxes, TTGNNN and TANNNT, respectively. We further analyzed spacer-lengths between the –35 and –10 boxes via a bioinformatics approach. The spacer-lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer-lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer-lengths indicated that the 11 bp spacer-length produced unusually high activity.
2020-01-26 | GSE143410 | GEO