Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing identifies O2-responsive genes in the human pathogenic fungus Aspergillus fumigatus

ABSTRACT: Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation ≈ 260 µmol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (≈ 13 µmol l-1).

ORGANISM(S): Aspergillus fumigatus

PROVIDER: GSE55943 | GEO | 2014/07/25

SECONDARY ACCESSION(S): PRJNA241401

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Next Generation Sequencing identifies O2-responsive genes in the human pathogenic fungus Aspergillus fumigatus

Project description:Low oxygen conditions are not only common to natural environments but also occur during tissue invasive growth in the human host. Only few cellular factors have been identified up to now that allow the fungus to efficiently adapt its energy metabolism to the lack of O2. In the present study, we cultivated A. fumigatus in an O2-controlled fermenter and analysed its minute-scale responses to O2 limitation. Transcriptome sequencing revealed a group of genes underlying a rapid and highly dynamic regulation. As an initial experimental setup, A. fumigatus was cultivated in an O2-controlled fermenter, which allowed minute-scale variations in O2-fluxes largely independent of other secondary effects. Cultures were initially grown at saturated O2 concentrations (100% saturation M-bM-^IM-^H 260 M-BM-5mol l-1) and rapidly shifted to hypoxic growth conditions at an initial O2 saturation of 5% (M-bM-^IM-^H 13 M-BM-5mol l-1). Dynamics of low and high O2 responses of A. fumigatus cultivated in an O2-controlled fermenter

2014-07-25 | E-GEOD-55943 | biostudies-arrayexpress

Synechocystis sp. proteome on differnt light conditions

Project description:Cyanobacteria are an integral part of the Earth’s biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2. Sustainable industrial applications, however, are still scarce and the true limits of phototrophic production remain unknown. One of the limitations of further progress is our insufficient understanding of the quantitative changes in photoautotrophic metabolism that occur during growth in dynamic environments. Uncovering principles of allocation of the key metabolites or proteins as a response to changing environment can provide significant advances in our understanding of phototrophic production limits. However, resolving such complex question requires multidisciplinary approach combining highly-controlled cyanobacteria cultivation coupled to quantitative analyses of specific cellular components. The following datase represents proteomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 that was cultivated in the well controlled environment of laboratory-scale photobioreactors in the quasi-continuous regime that allowed for maintaining the cells in the exponential growth phase. The sampels were taken under light-limited (25 - 220 µmol(photons) m-2 s-1), optimal (440 µmol(photons) m-2 s-1) and photoinhibited growth (1100 µmol(photons) m-2 s-1). Each culture was sampled in five biological replicates.

2019-01-07 | PXD009626 | Pride

Gene expression profile of HIF-1Î± silenced or non-silenced human DCs stimulated with A. fumigatus under normoxic or hypoxic conditions

Project description:DCs play a central role for the immune response against the mold Aspergillus fumigatus. Hypoxic microenvironments occur during infection with A. fumigatus. Hypoxia and signaling via hypoxia inducible factor 1Î± may modulate the response of DCs; however, the role in fungal infections is unclear. We used microarrays to determine the influence of hypoxia and HIF-1Î± signaling on the immune response of human DCs towards A. fumigatus. HIF-1Î± silenced or non-silenced, human monocyte-derived DCs were cultivated for 6 h in normoxia or hypoxia (1 % O2) without stimulation or stimulated with inactivated germ tubes of A. fumigatus. Three independent experiments with DCs derived from different blood donors were performed. RNA was extracted and hybridized on Affymetrix microarrays.

2015-11-01 | E-GEOD-60729 | biostudies-arrayexpress

Isolation of a novel heterodimeric PSII complex involved in PSII repair

Project description:The multi-subunit membrane protein complex Photosystem II (PSII) catalyzes the light driven oxidation of water and with this the initial step of photosynthetic electron transport in plants, algae, and cyanobacteria. Its biogenesis is coordinated by a network of auxiliary proteins that facilitate the stepwise assembly of individual subunits and cofactors, forming various intermediate complexes until fully functional mature PSII is present at the end of the process. In the current study, we purified PSII complexes from a mutant line of the thermophilic cyanobacterium Thermosynechococcus elongatus in which the extrinsic subunit PsbO, characteristic for active PSII, was fused with an N-terminal TwinStrep-Tag. Three distinct PSII complexes were separated by ion exchange chromatography after the initial affinity purification. Two complexes differ in their oligomeric state (monomeric and dimeric) but share the typical subunit composition of mature PSII. They are characterized by very high oxygen evolving activity of approx. 6,000 µmol O2· (mg Chl·h)-1. Analysis of the third (heterodimeric) PSII complex revealed lower oxygen evolving activity of approx. 3000 µmol O2· (mg Chl·h)-1 and a manganese content of 2.7 (± 0.2) per reaction center compared to 3.7 (± 0.2) of fully active PSII. Mass spectrometry and time-resolved fluorescence spectroscopy further indicated that PsbO is partially replaced by Psb27 in this PSII fraction, thus implying a role in repair of the complex.

2023-02-06 | PXD033676 | Pride

A Temporal Study of the Perturbation of Crustacean Neuropeptides Due to Severe Hypoxia Using 4-Plex Reductive Dimethylation

Project description:Hypoxia (i.e., low oxygen (O2) levels) is a common environmental challenge for several aquatic species, including fish and invertebrates. To survive or escape these conditions, these animals have developed novel biological mechanisms, some regulated by neuropeptides. By utilizing mass spectrometry, this study aims to provide a global perspective of neuropeptides in the blue crab, Callinectes sapidus, and their changes over time (0, 1, 4, and 8 hours) due to severe hypoxia (~10% O2 water saturation) stress using a 4-plex dimethyl labeling strategy to increase throughput. Using both electrospray ionization and matrix-assisted laser desorption/ionization provided complementary coverage– 88 neuropeptides were identified with only five overlapping between the two ionization techniques. Interesting trends include (1) an overall decrease in expression due to hypoxia exposure, (2) a return to basal levels after 4 or 8 hours of exposure following an initial response, (3) changes only after 4+ hours exposure, and (4) an oscillating pattern. Overall, this study boosts the power of multiplexed quantitation to understand the large-scale changes due to severe hypoxia stress over time.

2020-03-05 | PXD014688 | Pride

Multifaceted activity of cytokinin at distinct phases of leaf development shapes its size and structure in Arabidopsis thaliana

Project description:To get an insight into cytokinin-induced alterations of molecular networks underlying size and structure of a leaf, transgenic Arabidopsis lines (Col-0 background) CaMV35S>GR>ipt, and CaMV35S>GR>HvCKX2 were cultivated in a growth chamber under controlled environmental conditions (50-60% relative humidity, long day, 21/19 °C day/night temperature, 110 µmol m-2 s-1). Plants were activated at 14 DAS by watering once with 50 ml of distilled water supplemented with 10 µM dexamethasone dissolved in 5x10-4% (v/v) DMSO (DEX samples). Corresponding mock-treated control plants were watered with DMSO in water.

2019-02-21 | PXD007678 | Pride

Photophysiological and Genetic Factors Underlying Fast Photosynthetic Growth of Unicellular Cyanobacterium Synechococcus sp. PCC 7002

Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing the fast-growing response of Synechococcus sp. PCC 7002 response to variable irradience levels. We employed controlled cultivation and next-generation sequencing technology to identify transcriptional responses of euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 grown under steady state conditions at six irradiance levels ranging from 33 to 760 µmol photons m-2 sec-1.

2015-09-04 | E-GEOD-72691 | biostudies-arrayexpress

Long-term adaptation to hypoxic conditions - Febit transcriptome analysis

Project description:Aspergillus fumigatus is an opportunistic, airborne pathogen causing invasive aspergillosis in immunocompromised patients. During the infection process A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed significant increases in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification (fhpA), NAD+ regeneration (frdA, osmA) nitrogen metabolism (niaD, niiA) and respiration (rcfB). We show that the NO-detoxifying flavohemoprotein fhpA is strongly induced by hypoxia independent of the nitrogen source, but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD, the nitrite reductase gene niiA and the two fumarate reductases genes frdA and osmA, we found that alternative electron acceptors such as nitrate and fumarate do not have a significant impact on growth of A. fumigatus during hypoxia, but that functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complex III and IV play a crucial role in the hypoxic growth of A. fumigatus.

2014-07-01 | E-MTAB-2699 | biostudies-arrayexpress

Adaptation of Sulfolobus solfataricus P2 to fluctuating O2 concentrations

Project description:Sulfolobus solfataricus P2 was grown aerobically, with O2 concentrations ranging from 1.5 to 26 % (v/v; gas phase). To gain some insight in control of the respiratory system, transcriptomes of the strain cultivated in different O2 concentrations (1.5 % vs 21 %, 1.5 % vs 26 %) were compared using a DNA microarray approach.

2009-06-01 | GSE16043 | GEO

Effect of PT2385 treatment during cytotrophoblast differentiation under hypoxia

Project description:To investigate the therapeutic effect of HIF-2 inhibitor in placental dysfunction, we used primary cytotrophoblasts isolated from human placentas at term and cultured them under 2.5% O2 for 4 days. We either treated the cells with PT2385 at 10 µmol/L or vehicle and then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different placentas.

2022-10-31 | GSE216799 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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