Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA375085 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5262950_1.fastq.gz | Fastqsanger.gz | |||
| SRR5262950_2.fastq.gz | Fastqsanger.gz | |||
| SRR5262960_1.fastq.gz | Fastqsanger.gz | |||
| SRR5262960_2.fastq.gz | Fastqsanger.gz | |||
| SRR5262970_1.fastq.gz | Fastqsanger.gz |
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Project description:The Arabidopsis spaceflight transcriptome: a comparison of whole plants to discrete root, hypocotyl and shoot responses to the orbital environment
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Project description:Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural and metabolic differences between plants grown in space compared to plants on the Earth. Genes that are important in setting up the spaceflight responses are being identified; their role in spaceflight physiological adaptation are increasingly understood, and the fact that different genotypes adapt differently is recognized. However, the basic question of whether these spaceflight responses are required for survival has yet to be posed, and the fundamental notion that spaceflight responses may be non-adaptive has yet to be explored. Therefore the experiments presented here were designed to ask if portions of the plant spaceflight response can be genetically removed without causing loss of spaceflight survival and without causing increased stress responses. The CARA experiment compared the spaceflight transcriptome responses of two Arabidopsis ecotypes, Col-0 and WS, as well as that of a PhyD mutant of Col-0. When grown with the ambient light of the ISS, phyD displayed a significantly reduced spaceflight transcriptome response compared to Col-0, suggesting that altering the activity of a single gene can actually improve spaceflight adaptation by reducing the transcriptome cost of physiological adaptation. The WS genotype showed and even simpler spaceflight transcriptome response in the ambient light of the ISS, more broadly indicating that the plant genotype can be manipulated to reduce the transcriptome cost of plant physiological adaptation to spaceflight and suggesting that genetic manipulation might further reduce, or perhaps eliminate the metabolic cost of spaceflight adaptation. When plants were germinated and then left in the dark on the ISS, the WS genotype actually mounted a larger transcriptome response than Col-0, suggesting that the in-space light environment affects physiological adaptation, which further implies that manipulating the local habitat can also substantially impact the metabolic cost of spaceflight adaptation.
2017-06-14 | GSE94983 | GEO
Project description:Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware, and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves, hypocotyls and roots) and compared to analyses conducted with whole plants. Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis, however, closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment
2013-10-04 | E-MTAB-1264 | biostudies-arrayexpress
Project description:transcriptome response of Arabidopsis cultivar Columbia and WS whole plants and plant tissue roots, hypocotyls and shoots to the spaceflight environment Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware, and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves, hypocotyls and roots) and compared to analyses conducted with whole plants. Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis, however, closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment. This experiment was launched on STS-131 in 2010 and was supported by NASA grant NNX07AH27G - Transgenic Plant Biomonitors of Space Flight Exposure to R.J. Ferl and A-L. Paul.
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Project description:Crop plants are often exposed to the combination of drought and pathogen stress. Transcriptome studies on Arabidopsis thaliana and other plants unveiled activation of shared molecular defense mechanisms between under individual and combined stresses. These shared plant responses are characterized by commonly regulated genes under individual and combined stresses. Based on the previous studies, G-box binding factor 3 (GBF3) is one of the regulatory components of such shared responses. However, the mechanistic understanding on the role of GBF3 under combined drought and pathogen stress is not yet decoded. Using genetic approaches, we demonstrated Atgbf3 mutant plants are more susceptible under individual and combined drought and Pseudomonas syringae pv. tomato DC3000 stresses as compared to the wild-type plants. We further analyzed the global transcriptome of Atgbf3 mutant under combined stress to identify its downstream targets to further validate the role of AtGBF3 in combined stress. We used microarrays to detail the global transcriptome reprogramming during AtGBF3-mediated regulation of combined stress.
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Project description:The increasing availability of flights on suborbital rockets creates new avenues for the study of spaceflight effects on biological systems, in particular the transitions between hypergravity and microgravity. This paper presents an initial comparison of the responses of Arabidopsis thaliana to suborbital and atmospheric parabolic flights as an important step toward characterizing these emerging suborbital platforms and their effects on biology. Transcriptomic profiling of the response of the Arabidopsis ecotype Wassilewskija (WS) to the aggregate spaceflight experiences in the Blue Origin New Shepard and Virgin Galactic SpaceShipTwo rockets revealed that the transcriptomic load induced by flight differed greatly between the two flights, yet was biologically related to traditional parabolic flight responses. The sku5 skewing mutant and 14-3-3κ:GFP regulatory protein overexpression lines each showed altered intra-platform responses compared to WS in the Blue Origin and parabolic flights, respectively. An additional parabolic flight using the F-104 Starfighter showed that the response of 14-3-3κ:GFP to flight was modulated in a similar manner to the WS line. Despite the differing genotypes, experimental workflows, flight profiles and platforms, alteration of gene expression remodeling central metabolic processes was commonly observed as a response to the flights. The processes included carbon and nitrogen metabolism, branched-chain amino acid degradation, and hypoxic responses. The timing and directionality of differentially-expressed genes involved in the conserved pathways differed among the platforms. The data presented herein highlight the potential for various suborbital platforms to contribute insights into biological responses to spaceflight, and further suggest that in-flight fixation during suborbital experiments will provide insights into responses to each phase of flight.
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Project description:wip overexpressing plants-Transcriptome analysis of WIP overexpressing plants
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Project description:UV-B Responses in Light Grown Plants: Similarities to Biotic Stress
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