A. niger LC-MS/MS different carbon sources
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ FT
ORGANISM(S): Aspergillus Niger
SUBMITTER: 
Dorett Odoni
LAB HEAD: Vitor A. P. Martins dos Santos
PROVIDER: PXD004909 | Pride | 2016-11-28
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 20140203_MvD_WUR_1.raw.gz | Raw | |||
| 20140203_MvD_WUR_11.raw.gz | Raw | |||
| 20140203_MvD_WUR_12.raw.gz | Raw | |||
| 20140203_MvD_WUR_13.raw.gz | Raw | |||
| 20140203_MvD_WUR_17.raw.gz | Raw |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:The R. delemar strain ATCC 20344 was cultured under nitrogen starvation conditions with varied oxygen availability to induce high (aerobic) and low (anaerobic) fumarate production.
2017-02-15 | PXD004600 | Pride
Project description:To study the induction of the genes encoding known and putative enzymes from the pectinolytic system of A. niger, the transcriptional profiles of 58 selected known or putative pectinolytic genes were monitored by microarray experiments. For this purpose, A. niger was cultivated on the complex substrates, sugar beet pectin and polygalacturonic acid as primary carbon sources. Galacturonic acid, rhamnose and xylose were used to assess the effects on gene expression caused by simple well-defined carbon sources, representing the most abundant sugar residues present in the backbone of pectin. Fructose, as a strong repressor of the expression of genes that are under carbon catabolite regulation, and sorbitol, as a non-inducing sugar-like alcohol, which does not affect the carbon catabolite regulation mechanisms were selected as control substrates. Mycelia of A. niger were pregrown for 18 h on 2% fructose, transferred to medium containing the different pectic and control substrates, and sampled at four time points during 24 h of incubation.
2008-06-13 | E-MEXP-1626 | biostudies-arrayexpress
Project description:The genome of the filamentous fungus Aspergillus niger is rich in genes encoding pectinases, a broad class of enzymes that have been extensively studied due to their use in industrial applications. The sequencing of the A. niger genome provided more knowledge concerning the individual pectinolytic genes, but relatively little is still known about the regulatory genes involved in pectin degradation. Understanding regulation of the pectinolytic genes provides a tool to optimize the production of pectinases in this industrially important fungus. This study describes the identification and characterization of one of the activators of pectinase-encoding genes, RhaR. Inactivation of the gene encoding this regulator resulted in down-regulation of genes involved in the release and catabolism of L-rhamnose from the pectinolytic substructure rhamnogalacturonan I. We aim to discover differencial expressed genes in A.niger wild type strain N402 and M-NM-^TrhaR mutant while growing on rhamnose as carbon source. Biological duplicates were made for both strain at the growth of 2 hours, Affymetrix microarray experiments were performed on these samples.
2014-03-13 | E-GEOD-51023 | biostudies-arrayexpress
Project description:A. niger undergoes dramatic changes during asexual development. We tried to identify the differences in RNA expression levels that are important for this development. We used micro-arrays to determine which genes were up- or down-regulated in the aerial structures, the part of the colony that is formed during asexual development. A. niger was grown as a sandwiched culture (Wösten et al., 1991,Journal of General Microbiology 137: 2017–2023) in a 0.25 mm layer of 0.6 % agarose between two porous polycarbonate membranes (diameter 76 mm, pore size 0.1 µm; Profiltra; www.profiltra.nl). After six days of growth, the top membrane of the sandwich was replaced by a membrane with pores of 10 µm (Profiltra), allowing formation of aerial hyphae and conidiophores for 24 h. Vegetative mycelium and aerial structures of 7-day-old maltose-grown cultures of A. niger were harvested from 3 and 5 sandwiched colonies, respectively. The aerial structures were scraped from the top membrane of the sandwiched culture with a razor blade. From other colonies, vegetative mycelium was harvested by flipping over the top membrane and scraping it off with a razor blade.
2012-02-24 | E-GEOD-32123 | biostudies-arrayexpress
Project description:Microarray experiments were performed for identifying genes that are involved in inulin and sucrose metabolism by analyzing the transcriptomes of wild type strain N402 and inuR deletion strain grown in sucrose, as well as by analyzing the transcriptomes of wild type strain N402 grown in sucrose and xylose.
2008-06-01 | E-TABM-319 | biostudies-arrayexpress
Project description:Microarray experiments were performed for identifying genes that are involved in starch metabolism by analyzing the transcriptomes of wild type strain N402 and amyR deletion strain grown in maltose, as well as by analyzing the transcriptomes of wild type strain N402 grown in maltose and xylose.
2008-06-01 | E-TABM-324 | biostudies-arrayexpress
Project description:Interaction of microbes affects the growth, metabolism and differentiation of members of the community. While direct and indirect competitions, like spite and nutrient consumption have negative effect on each other, microbes also evolved in nature not only to fight, but in some cases to adapt or support each other while increasing the fitness of the community. Presence of bacteria and fungi in the soil results in interactions and various examples were described, including mutualism. Bacilli attach to the plant root and form complex communities in the rhizosphere. Bacillus subtilis, when grown in the presence of Aspergillus niger interacts with the fungal partner, attaches and grows on the hyphae. Using dual transcriptome experiment, we show that both fungi and bacteria alter their metabolisms during the interaction. Interestingly, the transcription of genes related to the antifungal and antibacterial defense mechanism of B. subtilis and A. niger, respectively, are decreased upon attachment of bacteria to the mycelia. Our microarray experiments provide a novel insight into the mutual interaction of a bacterium and a fungus. Aspergillus niger were grown with and without Bacillus subtilis. Biological triplicates were made for both conditions, Affymetrix microarray experiments were performed on these samples.
2014-10-07 | E-GEOD-46187 | biostudies-arrayexpress
Project description:Galactose catabolism in Aspergillus nidulans is regulated by at least two regulators, GalR and GalX. In Aspergillus niger only GalX is present, and its role in D-galactose catabolism in this fungus was investigated. Phenotypic and gene expression analysis of a wild type and a galX disruptant revealed that GalX does not substitute for the absence of GalR in A. niger, it regulates the D-galactose oxido-reductive pathway, but not the Leloir pathway. Four genes, including the recently characterized ladB (galactitol dehydrogenase) were found to have differencial expressions that are highly relevant to GalX , indicating a novel oxido-reductive pathway in A.niger . We aim to discover differentially expressed genes in A.niger wild type strain N402 and M-NM-^TgalX mutant while growing on galactose as carbon source. Biological duplicates were made for both strains. The strains were grown O/N in complete medium with 2% frunctose and mycelium was then washed and transferred to minimal medium with 25 mM D-galactose and incubated for 2 hours. Affymetrix microarray experiments were performed RNA isolated from these samples.
2012-09-20 | E-GEOD-40219 | biostudies-arrayexpress
Project description:Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. Eight samples in total consisting of duplicate shake flask Aspergillus niger cultures from four conditions: 48h glucose, 6 h starvation, 6 h wheat straw, 24 h starvation
2014-08-22 | E-GEOD-57315 | biostudies-arrayexpress
Project description:Knowledge of the biological and technical variation for fermentor-grown Aspergillus niger cultures is needed to design DNA microarray experiments properly. We cultured A. niger in batch-operated fermentor vessels and induced with D-xylose. Transcript profiles were followed in detail by qPCR for 8 genes. A variance components analysis was performed on these data to determine the origin and magnitude of variation within each process step for this experiment. 6 Fermentor cultures were selected to determine technical and biological variation for all 14554 ORFs present on this array type. Keywords: Validation of microarrays; variation analysis; experimental design For 5 weeks, 4 batch-fermentation per week were run in which A. niger was grown on 100 mM sorbitol. At 14 hours after oxygen supply had switched from headspace to sparger-inlet each fermentor was induced with either 0.1 mM D-xylose or 0.1 mM sorbitol. Samples were harvested just before induction and 1 hour after induction. Per week, 3 fermentors were induced with D-xylose and 1 fermentor was induced with sorbitol. Six samples were selected to be put on microarrays based on their biomass density, time distribution, magnitude of xylose-induced genes as measured by qPCR, fermentor vessel number.
2008-12-30 | E-GEOD-11405 | biostudies-arrayexpress