Ontology highlight
ABSTRACT:
PROVIDER: PRJNA605569 | ENA |
REPOSITORIES: ENA
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Project description:This study examined the functional response of a host (zebrafish) to implantation of a conspecific or allospecific (goldfish) gastrointestinal (GIT) microbiome followed by diet manipulation and the repercussions of these manipulations on host GIT physiology. Implantation of a native zebrafish biome successfully reintroduced wildtype (WT) communities with the exception of several rare, phylogenetically distant species. Implantation of a foreign goldfish biome created communities that were distinct from WT, suggesting that the seeding community created substantial differences from the native host communities. A mismatched ?natural? diet and an implanted allospecific biome enriched for rarer and more phylogenetically diverse bacteria. Transcriptional changes within the GIT clustered in relationship to biome treatments, mirroring clustering of biome implants. Implantation of an allospecific biome along with an altered diet markedly down-regulated approximately 70% of the transcripts involved in cholesterol biosynthesis, while tissue content analysis revealed an increase in total tissue cholesterol. Furthermore, transcripts involved in lipogenesis pathways were significantly downregulated and correlated with a striking decrease in intestinal lipase activity driven by both biome and diet. Glucose-6P dehydrogenase (G6PD) activities increased during dietary manipulations regardless of biome, while the allospecific biome down-regulated transcripts involved in gluconeogenesis and altered glucokinase (GK) and hexokinase (HK) activities regardless of diet. However, growth rates did not reveal an impact of these responses. Adult zebrafish are unable to reform proportional representation within bacterial communities following transplantation of an allospecific biome resulting in transcriptional and enzymatic alterations for lipid and carbohydrate metabolism that did not affect overall animal homeostasis.
2018-08-30 | GSE118496 | GEO
Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway.
2010-05-01 | GSE20487 | GEO
Project description:Purpose: To investigate the quaternary structures of Rhodopsin-family GPCRs. Method: Analyzed 60 receptors from HEK 293T cells. Results: 1) Most of these receptors are monomers. 2) The phylogenetic distribution of dimers suggests that monomers have an evolutionary advantage due to constraints imposed by dimerization on rates of receptor diversification.
2017-08-10 | GSE102461 | GEO
Project description:Synovial joint development begins with the formation of the interzone, a region of condensed mesenchymal cells at the site of the prospective joint. Recently, lineage tracing strategies have revealed that Gdf5-lineage cells native to and from outside the interzone contribute to most, if not all, of the major joint components. However, there is limited knowledge of the specific transcriptional and signaling programs that regulate interzone formation and fate diversification of synovial joint constituents. To address this, we have performed single cell RNA-Seq analysis of 7,329 synovial joint progenitor cells from the developing murine knee joint from E12.5 to E15.5. By using a combination of computational analytics, in situ hybridization, and in vitro characterization of prospectively isolated populations, we have identified the transcriptional profiles of the major developmental paths for joint progenitors. Our freely available single cell transcriptional atlas will serve as a resource for the community to uncover transcriptional programs and cell interactions that regulate synovial joint development.
2020-06-23 | GSE151985 | GEO
Project description:Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography
| PRJEB39010 | ENA
Project description:We report the single-cell transcriptional profiling of sea urchin primary mesenchyme cells isolated from embryos treated with DMSO or with 5-lox activating protein (FLAP) inhibitor MK-886. We find that inhibition of LOX activity with MK-886 prior to PMC isolation induces shifts in gene expression within the PMC population. We further demonstrate that control PMCs cluster into four transcriptionally-defined subsets, and MK-886-treated PMCs cluster into five distinct subsets. These data highlight novel transcriptional paradigms in the diversification of PMCs, and the requirement of ectodermal LOX activity for proper PMC transcriptional diversification.
2022-06-01 | GSE164240 | GEO
Project description:28 Streptomyces strains isolated from common scab lesions of potato tubers from a wide geographic range in Norway, were selected for microarray analysis. The selected strains were subjected to species identification by microarray, 16S phylogenetic analysis and PCR; and microarray-based comparative genome analysis. To our knowledge, this is the first report of S. turgidiscabies and S. europaeiscabiei in Norway. 28 Norwegian Streptomyces strains were hybridized in duplicates, one S.turgidiscabies strain (St32) and one S.scabies strain (ATCC49173) were hybridized in 4 replicates. Two out of 64 hybridizations failed (replicate hybridizations of Norwegian strains 33 and 44), for a total of 62 samples. Normalization was based on log-ratios against reference strain.
2010-04-30 | E-GEOD-20487 | biostudies-arrayexpress
Project description:Host shifts enhance diversification of the ectomycorrhizal fungal genus Strobilomyces
| PRJDB4146 | ENA
Project description:Activation of the extracellular signal regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states, named “L” and “R”, where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.
2024-03-20 | PXD048311 | Pride
Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes. Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates
2015-12-11 | E-GEOD-75873 | biostudies-arrayexpress