Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26125900_1.fastq.gz | Fastqsanger.gz | |||
| SRR26125900_2.fastq.gz | Fastqsanger.gz | |||
| SRR26125901_1.fastq.gz | Fastqsanger.gz | |||
| SRR26125901_2.fastq.gz | Fastqsanger.gz | |||
| SRR26125902_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:Corticosteroids have been prescribed for decades to modulate inflammation, yet there is a paucity of data on their effects in humans. We examined the changes in cellular and molecular immune system parameters, or âimmunome,â in 20 volunteers at baseline, and after intravenous hydrocortisone (HC) administered at moderate (250 mg) and low (50 mg) doses, to provide insight into how corticosteroids exert their effects. We observed declines in specific B and T cell subsets, and an increase in natural killer cell subsets 4-8 hours after HC. Whole transcriptome profiling revealed a gene expression signature that preceded lymphocyte population changes. We observed decreases in inflammatory cytokines after HC administration. Our study provides insights into the effects of corticosteroids on the human immunome. According to CHI protocols 11-H-0092, 18 healthy volunteers were administered a single dose of intravenous (IV) hydrocortisone at either 50 mg or 250 mg concentrations. PBMC samples were collected immediately prior to receiving the drug (0 hours), then after 1, 4, 8, 12, and 24 hours.
2016-03-14 | E-GEOD-67255 | biostudies-arrayexpress
Project description:Primary outcome(s): RNA from blood;Immunome analysis
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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:Corticosteroids have been prescribed for decades to modulate inflammation, yet there is a paucity of data on their effects in humans. We examined the changes in cellular and molecular immune system parameters, or “immunome,” in 20 volunteers at baseline, and after intravenous hydrocortisone (HC) administered at moderate (250 mg) and low (50 mg) doses, to provide insight into how corticosteroids exert their effects. We observed declines in specific B and T cell subsets, and an increase in natural killer cell subsets 4-8 hours after HC. Whole transcriptome profiling revealed a gene expression signature that preceded lymphocyte population changes. We observed decreases in inflammatory cytokines after HC administration. Our study provides insights into the effects of corticosteroids on the human immunome.
2016-03-14 | GSE67255 | GEO
Project description:We performed carefully designed and controlled animal feeding studies. We devided 9 adult rats in three group and each group fed with one type of diets in 28 days: rice, potatoes and chow. We fed piglets in triplicate either with cow milk or let them feed from sows milk for 4 weeks followed by 7 weeks of maize diet. Based on the small RNA sequencing data from 9 rat and 6 pig serum samples, we detected no transfer of plant miRNAs into rat blood, or bovine milk sequences into piglet blood.
2017-01-01 | GSE92897 | GEO
Project description:Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina x townsendii and Spartina anglica (Poaceae) Allopolyploidy results from two events: the merger of divergent genomes and genome duplication. Both events have important functional consequences for the evolution and adaption of newly formed allopolyploid species. In spite of significant progress made the last years, a few studies have decoupled the effects of hybridization from genome duplication in the observed patterns of expression changes accompanying allopolyploidy in natural conditions. We used Agilent Rice oligo-microarrays to explore gene expression changes following allopolyploidy in Spartina that includes a classical example of recent allopolyploid speciation, S. anglica formed during the 19th century following genome duplication of the hybrid S. x townsendii. Our data indicate important, thought different effects of hybridization and genome duplication in the expression patterns of the hybrid and allopolyploid. Deviation from parental additivity was most important following hybridization and was accompanied by maternal expression dominance, although transgressively expressed genes were also encountered. Maternal dominance is attenuated following genome duplication in S. anglica while this species exhibits an increased number of transgressively over expressed genes. These results reflect the decoupled effects of the “genomic shock” following hybridization and genome redundancy, on the genetic, epigenetic and regulatory mechanisms characterizing transcriptomic evolution in allopolyploids. We used Agilent Rice oligo-microarrays to explore gene expression changes among Spartina species, following interspesific hybridization and genome duplication (allopolyploidy). The analysed species included the parents S. maritima & S.alterniflora, the hybrid F1 S x. towensendii and the allopolyploid S.anglica. A total of 20 slides (five replicates per species) were hybridized on a 44 K Rice Agilent array using a one color desgin.
2010-11-10 | E-GEOD-18961 | biostudies-arrayexpress
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