Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA758440 | ENA |
REPOSITORIES: ENA
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Project description:The goals of these studies are to explore the mechanisms that enable extreme physiological plasticity and that may account for evolutionary divergence of adaptive osmotic physiologies among taxa that occupy different osmotic niches. In a common-garden environment, we track physiological and genome expression responses to hypo-osmotic (freshwater) challenge during a time-course of acclimation, and contrast these responses within and between species. We seek to identify mechanisms that facilitate osmotic acclimation that are evolutionarily conserved between basal and derived physiologies, and identify mechanisms that are uniquely derived to enable the extreme osmotic plasticity exhibited by F. heteroclitus. Importantly, previous studies using a comparable experimental design have identified physiological changes and genome expression responses that are adaptive for populations of F. heteroclitus that live in fresh water. As such, this enables us to test whether mechanisms of adaptive micro-evolutionary divergence across osmotic gradients within F. heteroclitus are shared with the mechanisms that account for patterns of macro-evolutionary divergence between F. heteroclitus and F. majalis that we identify in this study. That is, are the targets of micro-evolutionary fine-tuning the same or different as the targets of macro-evolutionary divergence across osmotic boundaries? Population comparisons include between populations from Chesapeake Bay (CB), coastal Virginia (VA), and coastal Georgia (GA).
2013-04-23 | E-MTAB-1551 | biostudies-arrayexpress
Project description:This study investigated the proteomes of macro-, micro- and nanovesicles derived from the same first trimester human placenta to better understand the role that these extracellular vesicles (EVs) play in maternal adaptation during healthy pregnancy. During human pregnancy, the mother undergoes major physiological and immunological adaptations to accommodate the fetus. There is growing evidence that EVs extruded from the placental syncytiotrophoblast into the maternal blood may regulate these maternal adaptations. Placental EVs can be divided into macro-, micro- and nanovesicles based on their size. To date, it is unclear whether these differently sized EVs carry different protein cargos and have different effects on maternal responses.
2016-04-29 | PXD003003 | Pride
Project description:Cell growth is controlled by nutrients and growth factors. How cells are regulated to enter stationary phase is still poorly understood. Previously we have identified 17 yeast genes whose expression is significantly up-regulated following starvation for different macro-nutrients. Here we demonstrate that activation of some of these genes is dependent on the Rim15 kinase and the Gis1 transcription factor. Phenotypic and microarray analyses reveal that Rim15p and Gis1p have both overlapping and distinct functions suggesting a non-linear relationship between the two. Subsequently we demonstrate that independent of Rim15p, TOR controls the limited proteolysis of Gis1p and regulates the binding of functional fragments to their target promoters. The limited proteolysis of Gis1p is executed by the proteasome to prevent its target genes from over activation. Thus, TOR regulates the function of the proteasome in response to nutrients so that gene expression is properly controlled, not only during active growth, but also in stationary phase.
2007-12-01 | E-MEXP-1139 | biostudies-arrayexpress
Project description:T helper 2 (Th2) responses protect against pathogens while also driving allergic inflammation, yet how large-scale Th2 responses are generated in tissue context remains unclear. Here, we used quantitative imaging to investigate early Th2 differentiation within lymph nodes (LNs) following cutaneous allergen administration. Contrary to current models, we observed extensive activation and ‘macro-clustering’ of early Th2 cells with migratory type-2 dendritic cells (cDC2s) generating specialized Th2-promoting microenvironments. Macro-clustering was integrin mediated and promoted localized cytokine exchange among T cells to reinforce differentiation, which contrasted behavior during Th1 responses. Unexpectedly, formation of Th2 macro-clusters was dependent on the site of skin sensitization. Differences between sites were driven by divergent activation states of migratory cDC2 from different dermal tissues, with enhanced costimulatory molecule expression by cDC2 in Th2-generating LNs promoting prolonged T cell activation, macro-clustering, and cytokine sensing. Thus, generation of dedicated Th2 priming microenvironments through enhanced costimulatory molecule signaling initiates Th2 responses in vivo and occurs in a skin site-specific manner.
2024-01-29 | GSE254473 | GEO
Project description:Intensity of press disturbance determined soil community stability to pulse disturbance
| PRJNA284605 | ENA
Project description:Benthic micro- and macro-community succession and coral recruitment under overfishing and nutrient enrichment
| PRJNA737519 | ENA
Project description:In a prior report, we observed two distinct lung microbiomes in healthy subjects that we termed “pneumotypes”: pneumotypeSPT, characterized by high bacterial load and supraglottic predominant taxa (SPT) such as the anaerobes Prevotella and Veillonella; and pneumotypeBPT, with low bacterial burden and background predominant taxa (BPT) found in the saline lavage and bronchoscope. Here, we determined the prevalence of these two contrasting lung microbiome types, in a multi-center study of healthy subjects. We confirmed that a lower airway microbiome enriched with upper airway microbes (pneumotypeSPT) was present in ~45% of healthy individuals.
2016-03-29 | GSE74395 | GEO
Project description:Transcript profiles of Laccaria bicolor S238N mycelium on various media were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor. We performed 15 hybridizations (Roche-NimbleGen) with samples derived from Laccaria bicolor free-living mycelium grown on MMN medium, on MMN with a 10 times reduction in all major macro-elements, on MMN with a 10 times reduction in the quantity of glucose or onto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments.
2012-03-01 | E-GEOD-35556 | biostudies-arrayexpress
Project description:Purpose: Helminth infection and dietary intake can affect the intestinal microbiota, as well as the immune system. Methods: Here we analyzed the relationship between fecal microbiota and blood profiles of indigenous Malaysians, referred to locally as Orang Asli, in comparison to urban participants from the capital city of Malaysia, Kuala Lumpur. Results: We found that helminth infections had a larger effect on gut microbial composition than did dietary intake or blood profiles. Trichuris trichiura infection intensity also had the strongest association with blood transcriptional profiles. By characterizing paired longitudinal samples collected before and after deworming treatment, we determined that changes in serum zinc and iron levels among the Orang Asli were driven by changes in helminth infection status, independent of dietary metal intake. Serum zinc and iron levels were associated with changes in the abundance of several microbial taxa. Conclusions: There is considerable interplay between helminths, micronutrients and the microbiota on the regulation of immune responses in humans.
2019-10-01 | GSE137338 | GEO