Ontology highlight
ABSTRACT:
PROVIDER: PRJNA761842 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15826963_1.fastq.gz | Fastqsanger.gz | |||
| SRR15826963_2.fastq.gz | Fastqsanger.gz | |||
| SRR15826964_1.fastq.gz | Fastqsanger.gz | |||
| SRR15826964_2.fastq.gz | Fastqsanger.gz | |||
| SRR15826965_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome analysis of Styrax tonkinensis under flood-drought abrupt alternation
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Project description:Using 3′-tiling microarray covering the rice genes, we carried out genome-wide expression analyses of total and polysome-fractionated samples treated with drought, salt and cold at 2-week-old rice leaves. compared to non-treated negative control (NC) samples. Our study is the first report which elucidated the global alternation of polysome association in response to abiotic stress. A total of 24 chips were used for microarray. At 2h, total and polysomal RNAs were extracted from drought, salt and cold at 2-week-old rice leaves with three biological replicates.
2012-03-02 | E-GEOD-32065 | biostudies-arrayexpress
Project description:Using 3′-tiling microarray covering the rice genes, we carried out genome-wide expression analyses of total and polysome-fractionated samples treated with drought, salt and cold at 2-week-old rice leaves. compared to non-treated negative control (NC) samples. Our study is the first report which elucidated the global alternation of polysome association in response to abiotic stress.
2012-03-02 | GSE32065 | GEO
Project description:The capacity of tumor cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways. Using an epithelial cancer model in Drosophila we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-basal cell polarity regulator, scribbled, and identified the cell fate regulator, Abrupt, a BTB-zinc finger protein. Abrupt overexpression alone is insufficient to transform cells, but in cooperation with scrib loss of function, Abrupt promotes the formation of massive tumors in the eye/antennal disc. The steroid hormone receptor coactivator, Taiman (SRC3/AIB1), is known to associate with Abrupt, and Taiman overexpression also drives tumor formation in cooperation with the loss of Scribbled. Expression arrays and ChIP-Seq indicates that Abrupt overexpression represses a large number of genes, including steroid hormone-response genes and multiple cell fate regulators, thereby maintaining cells within an epithelial progenitor-like state. The progenitor-like state is characterised by the failure to express the conserved Eyes absent/Dachshund regulatory complex in the eye disc, and in the antennal disc by the failure to express cell fate regulators that define the temporal elaboration of the appendage along the proximo-distal axis downstream of Distalless. Loss of scribbled promotes cooperation with Abrupt through impaired Hippo signaling, which is required and sufficient for cooperative overgrowth with Abrupt, and JNK signaling, which is required for tumor cell migration/invasion but not overgrowth. These results thus identify a novel cooperating oncogene, mammalian family members of which are also known oncogenes, and demonstrate that epithelial tumors in Drosophila can be characterised by the maintenance of a progenitor-like state. ChIP-Seq of Abrupt, ChIP-Seq of Abrupt (scrib-), Input, Input (scrib-)
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Project description:In plants, programmed cell death (PCD) is involved in both the development and in the response to biotic and abiotic aggressions. In early stages of PCD, mitochondrial membranes are made permeable by the formation of permeability transition pores, whose protein composition is debated. Since flooding stress can produce PCD in several plant species, the first goal of this work was to know if flooding stress could be used to induce PCD in Beta vulgaris roots. To do this, two months old beet plants were flood-stressed from one to five days, and the alterations indicating PCD in stressed beetroot cells were observed with a confocal fluorescence microscope. In addition, cytochrome c was released from mitochondria. After assessing that flood stress induced PCD in beetroots, the composition of mitochondrial protein complexes was observed in control and flood-stressed beetroots. Protein complexes from isolated mitochondria were separated by native gel electrophoresis, and their proteins were identified by mass spectrometry. The spectra count of three isoforms of voltage-dependent anion-selective channels (VDAC) increased after one day of flooding. In addition, the size of the complexes formed by VDAC was higher in beetroots flood-stressed for one day (~200 kDa) compared with non-stressed ones (~100 kDa). Other proteins, like chaperonin CPN60-2, also formed complexes with different masses in control and flood-stressed beetroots. Finally, possible interactions of VDAC with other proteins were found performing a cluster analysis. These results indicate that mitochondrial protein complexes formed by VDAC could be involved in the process of programmed cell death in flood-stressed beetroots
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Project description:Several methicillin resistance (SCCmec) clusters characteristic of hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) strains harbor the psm-mec locus. In addition to encoding the cytolysin, phenol-soluble modulin (PSM) mec, this locus has been attributed gene regulatory functions. Here we employed genome-wide transcriptional profiling to define the regulatory function of the psm-mec locus. The immune evasion factor protein A emerged as the primary conserved and strongly regulated target of psm-mec, an effect we show is mediated by the psm-mec RNA. Furthermore, the psm-mec locus exerted regulatory effects that were more moderate in extent and possibly mediated by the PSM-mec peptide. For example, expression of PSM-mec limited expression of mecA, thereby decreasing methicillin resistance. Our study shows that the psm-mec locus has a rare dual regulatory RNA and encoded cytolysin function, both with the potential to enhance MRSA virulence. Furthermore, our findings reveal a specific mechanism underscoring the recently emerging concept that S. aureus strains balance pronounced virulence and high expression of antibiotic resistance.
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Project description:Drought and heat are major abiotic stresses frequently coinciding to threaten rice production. Although hundreds of stress-related genes have been identified in the past two decades, very few genes have been confirmed to confer resistance to multiple stresses in crops. Here we report ONAC023, identified through NAC-centered gene regulatory network and genetic association analyses, is a hub stress-regulator that integrates the regulations of both drought and heat tolerance in rice. The loss-of-function mutant of ONAC023 showed significantly increased sensitivity to drought and heat stresses, whereas the overexpression of ONAC023 confers drought and heat tolerance at both seedling and reproductive stages. Notably, drought and heat stresses activated the function of ONAC023 not only by the induction of ONAC023 transcript but also by the nuclear accumulation of ONAC023 protein through a remorin-importin-α-assisted translocation. Under drought or heat stress, ONAC023 can directly target and promote the expression of functionally diverse downstream genes, such as OsPIP2;7, PGL3, OsFKBP20-1b, and OsSF3B1, which are involved in various stress-responsive processes including water transport, reactive oxygen species homeostasis, and alternative splicing (AS). Furthermore, genome-wide AS profiling revealed that the loss of ONAC023 function led to alternation of the encoding outcomes of thousands of AS transcripts under drought and heat stresses. These results manifested that ONAC023 is fine tuned to positively regulate drought and heat tolerance through the integration of multiple stress-responsive processes. Our findings provide not only an underlying connection between drought and heat responses, but also a promising candidate for engineering multi-stress-resilient rice.
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Project description:Purpose: Nonstructural carbohydrates has a major impact on trees response to meteorological conditions. The goals of this study were to define which changes in gene expression are linked to possible mechanisms used by the plant to buffer the decline in carbon source during gradual soil drying, an intensive abrupt heat wave, and recovery from drought? Methods: We combined measurements of nonstructural carbohydrates (NSC), tree physiology and expression of genes encoding starch metabolism enzymes. The experiment was conducted on potted olive (Olea europaea) trees, half of them under 28 days of soil drought. Results: We identified the gene family members relevant either to long-term or stress-induced carbon storage. Partitioning of expression patterns among β amylase’s and starch synthase’s family members were identified, with some members upregulated throughout drought while other members in recovery. The daily starch metabolism machinery was different from the stress-mode starch metabolism machinery when some genes are unique to the stress-mode response.
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