Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analysis of Neosartorya fischeri using different carbon sources, petroleum asphaltenes and glucose-peptone.

ABSTRACT: Asphaltenes are considered as the most recalcitrant petroleum fraction and represent a big problem for the recovery, separation and processing of heavy oils and bitumens. Neosartorya fischeri is a saprophytic fungus that is able to grow using asphaltenes as the sole carbon source [1]. We performed transcription profiling using a custom designed microarray with the complete genome from N. fischeri NRRL 181 in order to identify genes related to the transformation of asphaltenes [1]. Data analysis was performed using the genArise software. Results showed that 287 genes were up-regulated and 118 were down-regulated. Here we describe experimental procedures and methods about our dataset (NCBI GEO accession number GSE68146) and describe the data analysis to identify different expression levels in N. fischeri using this recalcitrant carbon source.

SUBMITTER: Hernandez-Lopez EL

PROVIDER: S-EPMC4583671 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Microarray analysis of Neosartorya fischeri using different carbon sources, petroleum asphaltenes and glucose-peptone.

Hernández-López Edna L EL Ramírez-Puebla Shamayim T ST Vazquez-Duhalt Rafael R

Genomics data 20150614

Asphaltenes are considered as the most recalcitrant petroleum fraction and represent a big problem for the recovery, separation and processing of heavy oils and bitumens. Neosartorya fischeri is a saprophytic fungus that is able to grow using asphaltenes as the sole carbon source [1]. We performed transcription profiling using a custom designed microarray with the complete genome from N. fischeri NRRL 181 in order to identify genes related to the transformation of asphaltenes [1]. Data analysis ...[more]

PMID: 26484261

Similar Datasets

Neosartorya fischeri Comparative Transcriptome when the fungi uses a differente carbon source, petroleum asphaltenes or glucose-peptona

Project description:Neosartorya fischeri is a fungi that is able to grow in petroleum asphaltenes as sole carbon source. Here, was investigated which enzymes were up regulated

2015-04-23 | GSE68146 | GEO

First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri.

Project description:A fungal strain isolated from a microbial consortium growing in a natural asphalt lake is able to grow in purified asphaltenes as the only source of carbon and energy. The asphaltenes were rigorously purified in order to avoid contamination from other petroleum fractions. In addition, most of petroporphyrins were removed. The 18S rRNA and β-tubulin genomic sequences, as well as some morphologic characteristics, indicate that the isolate is Neosartorya fischeri. After 11 weeks of growth, the fungus is able to metabolize 15.5% of the asphaltenic carbon, including 13.2% transformed to CO(2) . In a medium containing asphaltenes as the sole source of carbon and energy, the fungal isolate produces extracellular laccase activity, which is not detected when the fungus grow in a rich medium. The results obtained in this work clearly demonstrate that there are microorganisms able to metabolize and mineralize asphaltenes, which is considered the most recalcitrant petroleum fraction.

| S-EPMC3819015 | biostudies-literature

Comparison of Chemical Sensitivity of Fresh and Long-Stored Heat Resistant Neosartorya fischeri Environmental Isolates Using BIOLOG Phenotype MicroArray System.

Project description:Spoilage of heat processed food and beverage by heat resistant fungi (HRF) is a major problem for food industry in many countries. Neosartorya fischeri is the leading source of spoilage in thermally processed products. Its resistance to heat processing and toxigenicity makes studies about Neosartorya fischeri metabolism and chemical sensitivity essential. In this study chemical sensitivity of two environmental Neosartorya fischeri isolates were compared. One was isolated from canned apples in 1923 (DSM3700), the other from thermal processed strawberry product in 2012 (KC179765), used as long-stored and fresh isolate, respectively. The study was conducted using Biolog Phenotype MicroArray platforms of chemical sensitivity panel and traditional hole-plate method. The study allowed for obtaining data about Neosartorya fischeri growth inhibitors. The fresh isolate appeared to be much more resistant to chemical agents than the long-stored isolate. Based on phenotype microarray assay nitrogen compounds, toxic cations and membrane function compounds were the most effective in growth inhibition of N. fischeri isolates. According to the study zaragozic acid A, thallium(I) acetate and sodium selenate were potent and promising N. fischeri oriented fungicides which was confirmed by both chemical sensitivity microplates panel and traditional hole-plate methods.

| S-EPMC4729462 | biostudies-literature

Insight into the antifungal mechanism of Neosartorya fischeri antifungal protein.

Project description:Small, cysteine-rich, highly stable antifungal proteins secreted by filamentous Ascomycetes have great potential for the development of novel antifungal strategies. However, their practical application is still limited due to their not fully clarified mode of action. The aim of this work was to provide a deep insight into the antifungal mechanism of Neosartorya fischeri antifungal protein (NFAP), a novel representative of this protein group. Within a short exposure time to NFAP, reduced cellular metabolism, apoptosis induction, changes in the actin distribution and chitin deposition at the hyphal tip were observed in NFAP-sensitive Aspergillus nidulans. NFAP did show neither a direct membrane disrupting-effect nor uptake by endocytosis. Investigation of A. nidulans signalling mutants revealed that NFAP activates the cAMP/protein kinase A pathway via G-protein signalling which leads to apoptosis and inhibition of polar growth. In contrast, NFAP does not have any influence on the cell wall integrity pathway, but an unknown cell wall integrity pathway-independent mitogen activated protein kinase A-activated target is assumed to be involved in the cell death induction. Taken together, it was concluded that NFAP shows similarities, but also differences in its mode of antifungal action compared to two most investigated NFAP-related proteins from Aspergillus giganteus and Penicillium chrysogenum.

| S-EPMC4491047 | biostudies-literature

Functionality and prevalence of trehalose-based oligosaccharides as novel compatible solutes in ascospores of Neosartorya fischeri (Aspergillus fischeri) and other fungi.

Project description:Ascospores of Neosartorya, Byssochlamys and Talaromyces can be regarded as the most stress-resistant eukaryotic cells. They can survive exposure at temperatures as high as 85°C for 100?min or more. Neosartorya fischeri ascospores are more viscous and more resistant to the combined stress of heat and desiccation than the ascospores of Talaromyces macrosporus which contain predominantly trehalose. These ascospores contain trehalose-based oligosaccharides (TOS) that are novel compatible solutes, which are accumulated to high levels. These compounds are also found in other members of the genus Neosartorya and in some other genera within the order Eurotiales that also include Byssochlamys and Talaromyces. The presence of oligosaccharides was observed in species that had a relatively high growth temperature. TOS glasses have a higher glass transition temperature (Tg ) than trehalose, and they form a stable glass with crystallizing molecules, such as mannitol. Our data indicate that TOS are important for prolonged stabilization of cells against stress. The possible unique role of these solutes in protection against dry heat conditions is discussed.

| S-EPMC4371660 | biostudies-literature

Biofungicidal Potential of Neosartorya (Aspergillus) Fischeri Antifungal Protein NFAP and Novel Synthetic ?-Core Peptides.

Project description:Because of enormous crop losses worldwide due to pesticide-resistant plant pathogenic fungi, there is an increasing demand for the development of novel antifungal strategies in agriculture. Antifungal proteins (APs) and peptides are considered potential biofungicides; however, several factors limit their direct agricultural application, such as the high cost of production, narrow antifungal spectrum, and detrimental effects to plant development and human/animal health. This study evaluated the safety of the application of APs and peptides from the ascomycete Neosartorya fischeri as crop preservatives. The full-length N. fischeri AP (NFAP) and novel rationally designed ?-core peptide derivatives (PDs) ?NFAP-opt and ?NFAP-optGZ exhibited efficacy by inhibiting the growth of the agriculturally relevant filamentous ascomycetes in vitro. A high positive net charge, however, neither the hydrophilicity nor the primary structure supported the antifungal efficacy of these PDs. Further testing demonstrated that the antifungal activity did not require a conformational change of the ?-pleated NFAP or the canonically ordered conformation of the synthetic PDs. Neither hemolysis nor cytotoxicity was observed when the NFAP and ?NFAP-opt were applied at antifungally effective concentrations in human cell lines. Similarly, the Medicago truncatula plants that served as toxicity model and were grown from seedlings that were treated with NFAP, ?NFAP-opt, or ?NFAP-optGZ failed to exhibit morphological aberrations, reduction in primary root length, or the number of lateral roots. Crop protection experiments demonstrated that NFAP and associated antifungal active ?-core PDs were able to protect tomato fruits against the postharvest fungal pathogen Cladosporium herbarum.

| S-EPMC7237641 | biostudies-literature

Structural determinants of Neosartorya fischeri antifungal protein (NFAP) for folding, stability and antifungal activity.

Project description:The recent global challenges to prevent and treat fungal infections strongly demand for the development of new antifungal strategies. The structurally very similar cysteine-rich antifungal proteins from ascomycetes provide a feasible basis for designing new antifungal molecules. The main structural elements responsible for folding, stability and antifungal activity are not fully understood, although this is an essential prerequisite for rational protein design. In this study, we used the Neosartorya fischeri antifungal protein (NFAP) to investigate the role of the disulphide bridges, the hydrophobic core, and the N-terminal amino acids in the formation of a highly stable, folded, and antifungal active protein. NFAP and its mutants carrying cysteine deletion (NFAPΔC), hydrophobic core deletion (NFAPΔh), and N-terminal amino acids exchanges (NFAPΔN) were produced in Pichia pastoris. The recombinant NFAP showed the same features in structure, folding, stability and activity as the native protein. The data acquired with mass spectrometry, structural analyses and antifungal activity assays of NFAP and its mutants proved the importance of the disulphide bonding, the hydrophobic core and the correct N-terminus for folding, stability and full antifungal function. Our findings provide further support to the comprehensive understanding of the structure-function relationship in members of this protein group.

| S-EPMC5434006 | biostudies-literature

Aspergillus flavus grown in peptone as the carbon source exhibits spore density- and peptone concentration-dependent aflatoxin biosynthesis.

Project description:BACKGROUND: Aflatoxins (AFs) are highly carcinogenic compounds produced by Aspergillus species in seeds with high lipid and protein contents. It has been known for over 30 years that peptone is not conducive for AF productions, although reasons for this remain unknown. RESULTS: In this study, we showed that when Aspergillus flavus was grown in peptone-containing media, higher initial spore densities inhibited AF biosynthesis, but promoted mycelial growth; while in glucose-containing media, more AFs were produced when initial spore densities were increased. This phenomenon was also observed in other AF-producing strains including A. parasiticus and A. nomius. Higher peptone concentrations led to inhibited AF production, even in culture with a low spore density. High peptone concentrations did however promote mycelial growth. Spent medium experiments showed that the inhibited AF production in peptone media was regulated in a cell-autonomous manner. mRNA expression analyses showed that both regulatory and AF biosynthesis genes were repressed in mycelia cultured with high initial spore densities. Metabolomic studies revealed that, in addition to inhibited AF biosynthesis, mycelia grown in peptone media with a high initial spore density showed suppressed fatty acid biosynthesis, reduced tricarboxylic acid (TCA) cycle intermediates, and increased pentose phosphate pathway products. Additions of TCA cycle intermediates had no effect on AF biosynthesis, suggesting the inhibited AF biosynthesis was not caused by depleted TCA cycle intermediates. CONCLUSIONS: We here demonstrate that Aspergillus species grown in media with peptone as the sole carbon source are able to sense their own population densities and peptone concentrations to switch between rapid growth and AF production. This switching ability may offer Aspergillus species a competition advantage in natural ecosystems, producing AFs only when self-population is low and food is scarce.

| S-EPMC3412747 | biostudies-literature

Ageing transcriptomes of selected mutants on different carbon sources

Project description:Here we show that an unrestricted galactose diet in early life minimises pathology during replicative ageing in budding yeast, irrespective of diet later in life. Lifespan and average mother cell division rate are comparable between glucose and galactose diets, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing these to be facets of ageing pathology rather than intrinsic parts of the replicative ageing process. Respiration on galactose is critical for minimising ageing pathology, and forced respiration during ageing on glucose by over-expression of Hap4 also has the same effect though only in a fraction of cells. This fraction maintains Hap4 activity to advanced age with low senescence and a youthful gene expression profile, whereas other cells in the same population that lose Hap4 activity undergo dramatic dysregulation of gene expression and accumulate aneuploid fragments of chromosome XII aneuploidy (ChrXIIr), which are tightly associated with ageing pathology.

2022-07-21 | GSE207503 | GEO

Transcriptome response to different carbon sources in Acetobacter aceti

Project description:Acetic acid bacteria are obligately aerobic alphaproteobacteria that have a unique ability to incompletely oxidize various alcohols and sugars to organic acids. The ability of these bacteria to incompletely oxidize ethanol to acetate has been historically utilized for vinegar production. The mechanism of switching between incomplete oxidation and assimilatory oxidation and the control of energy and carbon metabolism in acetic acid bacteria are not fully understood. To understand the physiology and molecular biology of acetic acid bacteria better, we determined the draft genome sequence of Acetobacter aceti NBRC 14818, which is the type strain of the genus. Based on this draft genome sequence, the transcriptome profiles in A. aceti cells grown on ethanol, acetate, glucose, or mix of ethanol and glucose was determined by using NimbleGen Prokaryotic Expression array (4x72K).

2011-01-17 | GSE24361 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data