Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus
Ontology highlight
ABSTRACT:
ORGANISM(S): Aspergillus cristatus
SUBMITTER: zuo-yi Liu
PROVIDER: E-GEOD-65662 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The purpose of this study is to find the differently expressed genes in Aspergillus cristatus at different osmotic pressure.
2016-09-01 | GSE65662 | GEO
Project description:we studied the gene expression conditions while Drechslerella stenobrocha predates Caenorhabditis elegans. The perpose of this study is to find genes in Drechslerella stenobrocha participateing in predation. Examination of 3 transcriptomes in different predation periods to find their different gene expression style.
2014-01-28 | E-GEOD-54423 | biostudies-arrayexpress
Project description:Cerebrovascular dysfunction is a hallmark feature of Alzheimer's disease (AD). One of the greatest risk factor for AD is the apolipoprotein E4 (E4) allele. APOE4 genotype has been shown to negatively impact on perivascular amyloid clearance, however, its direct influence along with the other APOE variants (APOE2 and APOE3) on the molecular integrity of the cerebrovasculature has not been largely explored. To address this, we employed a 10-plex tandem isobaric mass tag approach in combination with an ultra-high pressure liquid chromatography MS/MS (Q-Exactive) method, to interrogate unbiased proteomic changes in cerebrovessels from AD and healthy control brains on different APOE genotype backgrounds. We first interrogated changes between healthy control homozygote E2/E2, E3/E3 and E4/E4 cases to identify underlying genotype specific effects on cerebrovessels. EIF2 signaling, regulation of eIF4 and 70S6K signaling and mTOR signaling were the top significantly altered pathways in E4/E4 compared to E3/E3 cases. EIF2, nitric oxide and sirtuin signaling pathways were the top significantly altered pathways in E4/E4 compared to E2/E2 cases. We used a Two-way ANOVA analysis to identify AD-dependent changes and their interactions with APOE genotype. The highest number of significantly regulated proteins from this interaction was observed in E3/E4 (192) and E4/E4 (189) cases. As above, EIF2, mTOR signaling and eIF4 and 70S6K signaling were the top three significantly altered pathways in E4 allele carriers (i.e. E3/E4 and E4/E4 genotypes). Of all the cerebrovascular cell specific markers identified in our proteomic analyses, endothelial cell, astrocyte, and smooth muscle cell specific protein markers were significantly altered in E4/E4 cases, while endothelial cells and astrocyte specific protein markers were altered in E3/E4 cases. These proteomic changes provide novel insights to explain the longstanding link between APOE4 and cerebrovascular dysfunction. The early and converging APOE4 dependent changes we identified could provide novel targets in the cerebrovasculature for developing disease modifying strategies to mitigate the effects of APOE4 genotype on increasing the risk for, and the path towards AD pathogenesis.
2021-03-23 | PXD023340 | Pride
Project description:Series containes 4 independent experiments and high and low power scanns for each independent experiment. Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized. We selected a hydrostatic pressure of 30 MPa at 25°C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression. Functional characterization of pressure-induced genes suggests that genes involved in protein metabolism and membrane metabolism were induced. The response to 30 MPa was significantly different from that observed under lethal conditions because protein degradation was not activated under 30 MPa pressure. Strongly induced genes included those that contribute to membrane metabolism and which are also induced by detergents, oils, and membrane stabilizers.
2010-06-10 | E-GEOD-2526 | biostudies-arrayexpress
Project description:In a context of climate change, deciphering signaling pathways leading to plant adaptation to drought, water availability, and salt tolerance is a crucial question. A common crossing point of these plant stresses is their impact on plant water potential, a composite physico-chemical variable reflecting the availability of water for the plant biological and biochemical processes such as growth or stomatal aperture. The water potential of plant cells is mainly driven by their turgor pressure and osmotic potential. Here we investigated the effect of a variety of osmotic treatments in the root of Arabidopsis plants grown in hydroponics. Measurement of the cortical cells turgor pressure with a cell pressure probe allowed to control the intensity of the treatments and, in particular, preserve the cortex from plasmolysis. Transcriptome analyses at early time point (15min) showed specific and quantitative transcriptomic responses for both osmotic and turgor pressures in the root. Our results highlight how water-related biophysical parameters can shape the transcriptome and provide putative candidates to explore further the early perception of water stress in plants.
2023-09-11 | GSE223207 | GEO
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
Project description:We report Hedgehog signaling responsive genes with or without Esrrb in NI3T3 cells. Using Hh-responsive cells, we used RNA-Seq to find Hh responsive genes. In addition, we tested Esrrb's modification on Hh target genes' response. Control vector transfected cells with vehicle treatment, Esrrb expression vector transfected cell with vehicle treatment, control vector transfected cells with Hh conditioned medium treatment, Esrrb expression vector transfected cell with Hh conditioned medium treatment,
2015-11-06 | E-GEOD-71209 | biostudies-arrayexpress
Project description:Talemi2016 - Yeast osmo-homoestasis
This model is described in the article:
Systems Level Analysis of
the Yeast Osmo-Stat.
Talemi SR, Tiger CF, Andersson M,
Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J.
Sci Rep 2016; 6: 30950
Abstract:
Adaptation is an important property of living organisms
enabling them to cope with environmental stress and maintaining
homeostasis. Adaptation is mediated by signaling pathways
responding to different stimuli. Those signaling pathways might
communicate in order to orchestrate the cellular response to
multiple simultaneous stimuli, a phenomenon called crosstalk.
Here, we investigate possible mechanisms of crosstalk between
the High Osmolarity Glycerol (HOG) and the Cell Wall Integrity
(CWI) pathways in yeast, which mediate adaptation to hyper- and
hypo-osmotic challenges, respectively. We combine ensemble
modeling with experimental investigations to test in
quantitative terms different hypotheses about the crosstalk of
the HOG and the CWI pathways. Our analyses indicate that for
the conditions studied i) the CWI pathway activation employs an
adaptive mechanism with a variable volume-dependent threshold,
in contrast to the HOG pathway, whose activation relies on a
fixed volume-dependent threshold, ii) there is no or little
direct crosstalk between the HOG and CWI pathways, and iii) its
mainly the HOG alone mediating adaptation of cellular osmotic
pressure for both hyper- as well as hypo-osmotic stress. Thus,
by iteratively combining mathematical modeling with
experimentation we achieved a better understanding of
regulatory mechanisms of yeast osmo-homeostasis and formulated
new hypotheses about osmo-sensing.
This model is hosted on
BioModels Database
and identified by:
MODEL1606100000.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2017-05-18 | MODEL1606100000 | BioModels
Project description:The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions and confirmed most of the annotated genes. Moreover, with high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons (uATGs) and upstream open reading frames (uORFs), which serves a remarkable insight into the A. oryzae transcriptome. We also were able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes or pathways that might involve in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae was much more complex than previously anticipated and the results might provide a blueprint for further study of A. oryzae transcriptome. mRNA expression of Aspergillus oryzae in 4 different culture conditions was determined by method of RNA-Seq using short reads from high throughput sequencing technology.
2010-02-02 | E-GEOD-18851 | biostudies-arrayexpress
Project description:Pipecolic acid or L-PA is a cyclic amino acid derived from L-lysine which has gained interest in the recent years within the pharmaceutical and chemical industries. L-PA can be produced efficiently using recombinant Corynebacterium glutamicum strains by expanding the natural L-lysine biosynthetic pathway. We show that de novo synthesized or externally added L-PA partially is beneficial for growth under hyper-osmotic stress conditions. C. glutamicum cells accumulated L-PA under elevated osmotic pressure and released it after an osmotic down shock. The proline permease ProP was identified as a candidate L-PA uptake system since RNAseq analysis revealed increased proP RNA levels upon L-PA production
2019-05-31 | GSE122249 | GEO