Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1259446 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33449403_1.fastq.gz | Fastqsanger.gz | |||
| SRR33449403_2.fastq.gz | Fastqsanger.gz | |||
| SRR33449404_1.fastq.gz | Fastqsanger.gz | |||
| SRR33449404_2.fastq.gz | Fastqsanger.gz | |||
| SRR33449405_1.fastq.gz | Fastqsanger.gz |
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Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. nirS gene diversity from two salt marsh experiments, GSM (4 treatments, 8 samples, duplicate arrays, four replicate blocks per array, 8 arrays per slide) and PIE (2 treatments, 16 samples, duplicate arrays four replicate blocks per array, 8 arrays per slide)
2010-11-13 | E-GEOD-25227 | biostudies-arrayexpress
Project description:Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated microbial community profiles as well as directly assayed nitrogen cycling genes that encode the enzymes responsible for overall nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms responsible for production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that elevated rates of nitrous oxide production and consumption are the result of changes in community structure, not simply changes in microbial activity.
2018-01-13 | GSE108888 | GEO
Project description:Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply, despite demonstrable and diverse nutrient–induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.
2010-11-13 | GSE25227 | GEO
Project description:Vibrio natriegens is a rapidly growing salt marsh bacterium that is being developed as a synthetic biology chassis. We characterized its physiological response to different salinities and temperatures in order to optimize culturing conditions and understand its adaptations to a salt marsh environment. Using metabolomics, transcriptomics, and proteomics we determined what pathways respond to these environmental parameters. We found that organic osmolyte synthesis and membrane transporters were most responsive to changes in salinity. The primary osmolytes were glutamate, glutamine, and ectoine, responding to salinity across temperature treatments. However, when media was supplemented with choline, glycine betaine seemed to mostly replace ectoine. These results provide a baseline dataset of metabolic activity under a variety of conditions that will inform decisions made about culturing and genome engineering for future applications.
2021-09-15 | PXD027874 | Pride
Project description:Hybridisation plays a significant role in the evolution and diversification of plants. Hybridisation among Nepenthes species is extensive, either naturally or man-made. To investigate the effects of hybridisation on the chemical compositions, we carried out metabolomics study on pitcher tissue of Nepenthes ampullaria, Nepenthes rafflesiana and their hybrid, Nepenthes × hookeriana. Pitcher samples were harvested and extracted in methanol:chloroform:water via sonication-assisted extraction before analysed using LC-TOF-MS. MS data were analysed using XCMS online version 2.2.5. This is the first MS data report towards the profiling, identification and comprehensive comparison of metabolites present in Nepenthes species.
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Project description:we want to test how different diets (high energy diet HED and low energy diet LED) alter muscle methabolism in pigs. we perform different array experiments using an human platform (GPL2011) and RNA extracted from pig skelethal muscle. thank's this we also test cross-species hybridisation. Keywords: comparative genomic hybridisation
2005-08-31 | GSE2785 | GEO
Project description:AIMS: HER2 testing of invasive breast cancer by in-situ hybridisation guides therapy decisions. Probing HER2 and cen17 simultaneously is supposed to reveal both a potential HER2 gene amplification and polysomy 17. However, a considerable number of breast cancer patients with quasi polysomy 17 are considered "equivocal" which is diagnostically meaningless. Moreover, patients with equivocal / false polysomic tumours are prevented from a potentially beneficial anti-HER2 treatment. Here we evaluated the RAI1, D17S122, and TP53 hybridisation markers to reliably indicate true polysomy and to accurately reclassify equivocal samples as HER2-positive. METHODS AND RESULTS: Samples with (n = 82) and without (n = 52) increased cen17 copy numbers and 78 evidently HER2-amplified specimens were analysed using dual and triple marker hybridisation probes. Selected putative polysomic samples were subjected to array-based comparative genomic hybridisation. We found that 37.8% samples with putative polysomy 17 did not show any gain in RAI1, D17S122, or TP53. Accordingly, aCGH revealed evidence for the presence of HER2/cen17 coamplification rather than for true polysomy in those cases. Reflex testing using alternate 17p markers reclassified up to 56.3% equivocal cases as HER2-positive and the combined assessment of a 17p and 17q locus allows the differentiation of true vs. false polysomy. CONCLUSIONS: An increased cen17 copy number does not necessarily reflect polysomy and reflex testing facilitates the reclassification of "equivocals". Nevertheless, the prognostic and predictive value of a HER2/cen17 coamplification versus HER2 gene amplification alone must still be prospectively evaluated. This article is protected by copyright. All rights reserved.
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