Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Arabidopsis thaliana tritrophic interaction experiment

ABSTRACT: Multi-species interactions are a major force in the evolution and dynamics of ecosystems. These interactions may occur either when species affect each other directly or when they interact indirectly via an intermediary species. Direct interactions between species are best understood, but indirect interactions may also often be strong enough to alter the evolutionary trajectories of the target species. Little is known about the genetic basis of direct interactions within an ecosystem and even less data is available for indirect interactions. This experiment uses a simple model ecosystem to build a view at the transcriptome level of how interactions between plants (Arabidopsis) and rhizosphere bacteria (Pseudomonas) are altered by biotic stressors (insect herbivores) and abiotic stressors (UV-B). Keywords: stress response

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE4973 | GEO | 2008/11/25

SECONDARY ACCESSION(S): PRJNA95475

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Transcription profiling of Arabidopsis thaliana tritrophic interaction

Project description:Multi-species interactions are a major force in the evolution and dynamics of ecosystems. These interactions may occur either when species affect each other directly or when they interact indirectly via an intermediary species. Direct interactions between species are best understood, but indirect interactions may also often be strong enough to alter the evolutionary trajectories of the target species. Little is known about the genetic basis of direct interactions within an ecosystem and even less data is available for indirect interactions. This experiment uses a simple model ecosystem to build a view at the transcriptome level of how interactions between plants (Arabidopsis) and rhizosphere bacteria (Pseudomonas) are altered by biotic stressors (insect herbivores) and abiotic stressors (UV-B). Experiment Overall Design: Arabidopsis plants were established and then split into two cohorts at 15 days. One group were innoculated with Pseudomonas aeruginosa strain 7NR and the other not. 21 days later half of each of these groups were subjected to UV-B treatment for seven days. After this period each of the four groups of plants were further subdivided and infested with aphids, caterpillars or left alone. 24 hours after infestation the plants were harvested, individuals pooled and total RNA extracted giving 12 unique conditions. Five replicates were performed in series, yielding a total of 60 samples.

2008-11-29 | E-GEOD-4973 | biostudies-arrayexpress

Metaproteomic data of maize rhizosphere

Project description:We present metaproteome data from maize rhizosphere from sodic soil. Isolation of proteome from maize rhizosphere collected from Experimental Farm, ICAR-IISS, Mau, India was done with the standardized protocol at our laboratory and metaproteome analysis was done with the standardized pipepline. In total 696 proteins with different functions representing 245 genus and 395 species were identified. The proteome data provides direct evidence on the biological processes in soil ecosystem and is the first reported reference data from maize rhizosphere.

2019-10-08 | PXD014519 | Pride

LC-MSMS analysis of muscle in the European pilchard depending on pollutant levels

Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse muscle proteome of wild European pilchards evolving in the Mediterranean Sea with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.

2024-01-30 | PXD037313 | Pride

LC-MSMS analysis of muscle in the gilt-head sea bream depending on pollutant levels

Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse muscle proteome of wild gilt-head sea bream evolving in the Mediterranean Sea (coastal area) with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.

2025-03-17 | PXD037412 | Pride

LC-MSMS analysis of liver in the gilt-head sea bream depending on pollutant levels

Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse liver proteome of wild gilt-head sea bream evolving in the Mediterranean Sea (coastal area) with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.

2025-03-17 | PXD037424 | Pride

LC-MSMS analysis of liver in the European pilchard depending on pollutant levels

Project description:The oceans are now all affected by human activities. The study of the impact of pollution on the health status of exploited marine populations is essential to better understand the direct constraints that stress generates on growth, reproduction, immune system and, ultimately, on the reproductive success of animals. Interactions between different stressors can generate non-additive effects ("cocktail effects"), which makes experimental models under controlled conditions based on only one or a few "stressors" insufficient. Thus, quantitative proteomics was used to analyse liver proteome of wild European pilchards evolving in the Mediterranean Sea with contrasting levels of organic and inorganic contamination. The prospects of researching biomarkers of health status that can be used as indicators of the status of a population or an ecosystem are of major interest for the monitoring and management of natural environments, hence promoting the conservation and management of marine species.

2024-01-30 | PXD037276 | Pride

GNPS coral-algae laboratory interaction experiments

Project description:These samples were generated during a laboratory experiment at SIO in which Acropora yongei (coral) were placed into direct and indirect interactions with two species of algae, another species of coral, and cold temperatures. Mass Spec run by Rob Quinn.

2015-04-01 | MSV000079091 | GNPS

Habitat diversity and multifunctionality

Project description:Habitat diversity and ecosystem multifunctionality - the importance of direct and indirect effects

| PRJEB17981 | ENA

Symbiosis induces widespread changes in the proteome of the model cnidarian Aiptasia

Project description:Coral reef ecosystems are metabolically founded on the mutualism between corals and photosynthetic dinoflagellates of the genus Symbiodinium. The glass anemone Aiptasia sp. has become a tractable model for this symbiosis. We utilized label-free liquid chromatography electrospray-ionization tandem mass spectrometry to analyze the effects of symbiosis on the proteomes of symbiotic and aposymbiotic Aiptasia. We quantified more than 3,300 proteins in 1,578 protein clusters, with 81 protein clusters showing significantly different expression. Symbiotic anemones showed higher expression of proteins involved in lipid storage and transport, nitrogen transport and cycling, intracellular trafficking, endocytosis and inorganic carbon transport. These changes reflect shifts in host metabolism and energy reserves due to increased organic and inorganic nutritional exchange with the symbionts. Aposymbiotic anemones exhibited increased expression of multiple systems responsible for mediating reactive oxygen stress, suggesting that the host derives direct or indirect protection from oxidative stress while in symbiosis. Aposymbiotic anemones also increased their expression of an array of proteases and chitinases, indicating a metabolic shift from autotrophy to heterotrophy. These results provide a comprehensive Aiptasia proteome with more direct relative quantification of protein abundance than transcriptomic methods, allowing more powerful studies of coral physiology and ecosystem function.

2017-02-22 | PXD003202 | Pride

The metabolic response of marine copepods to environmental warming and ocean acidification in the absence of food

Project description:Marine copepods are central to the productivity and biogeochemistry of marine ecosystems. Nevertheless, the direct and indirect effects of climate change on their metabolic functioning remain poorly understood. Here, we use metabolomics, the unbiased study of multiple low molecular weight organic metabolites, to examine how the physiology of Calanus spp. is affected by end-of-century global warming and ocean acidification scenarios. We report that the physiological stresses associated with incubation without food over a 5-day period greatly exceed those caused directly by seawater temperature or pH perturbations. This highlights the need to contextualise the results of climate change experiments by comparison to other, naturally occurring stressors such as food deprivation, which is being exacerbated by global warming. Protein and lipid metabolism were up-regulated in the food-deprived animals, with a novel class of taurine-containing lipids and the essential polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid and docosahexaenoic acid, changing significantly over the duration of our experiment. Copepods derive these PUFAs by ingesting diatoms and flagellated microplankton respectively. Climate-driven changes in the productivity, phenology and composition of microplankton communities, and hence the availability of these fatty acids, therefore have the potential to influence the ability of copepods to survive starvation and other environmental stressors.

2015-10-13 | MTBLS91 | MetaboLights

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