Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1072066 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole Genome of Hooded Vulture (Necrosyrtes monachus) and White-Backed Vulture (Gyps africanus)
| PRJEB66334 | ENA
Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.
2019-07-30 | E-MTAB-7771 | biostudies-arrayexpress
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. ZIKV infections are associated with neurodevelopmental deficiencies termed Congenital Zika Syndrome. ZIKV strains are grouped into three phylogenetic lineages: East African, West African, and Asian, which contains the American lineage. RNA virus genomes exist as genetically-related sequences. The heterogeneity of these viral populations is implicated in viral fitness, and genome diversity is correlated to virulence. This study examines genetic diversity of representative ZIKV strains from all lineages utilizing next generation sequencing (NGS). Inter-lineage diversity results indicate that ZIKV lineages differ broadly from each other; however, intra-lineage comparisons of American ZIKV strains isolated from human serum or placenta show differences in diversity when compared to ZIKVs from Asia and West Africa. This study describes the first comprehensive NGS analysis of all ZIKV lineages and posits that sub-consensus-level diversity may provide a framework for understanding ZIKV fitness during infection.
2018-12-31 | E-MTAB-5945 | biostudies-arrayexpress
Project description:Naïve T cells respond to antigen stimulation by exiting from quiescence into clonal expansion and functional differentiation, but the control mechanism is elusive. Here we describe that Raptor/mTORC1-dependent metabolic reprogramming is a central determinant of this transitional process. Loss of Raptor abrogates T cell priming and Th2 cell differentiation, although Raptor function is less important for continuous proliferation of actively cycling cells. mTORC1 coordinates multiple metabolic programs in T cells including glycolysis, lipid synthesis and oxidative phosphorylation to mediate antigen-triggered exit from quiescence. mTORC1 further links glucose metabolism to the initiation of Th2 differentiation by orchestrating cytokine receptor expression and cytokine responsiveness. Activation of Raptor/mTORC1 integrates T cell receptor (TCR) and CD28 co-stimulatory signals in antigen-stimulated T cells. Our studies identify a Raptor/mTORC1-dependent pathway linking signal-dependent metabolic reprogramming to quiescence exit, and this in turn coordinates lymphocyte activation and fate decisions in adaptive immunity. We used microarrays to explore the gene expression profiles differentially expressed in CD4+ T-cells from wild-type (WT) and CD4(cre) x Raptor(fl/fl) mice before and after stimulation with anti CD3/CD28 antibodies.
2014-01-27 | E-GEOD-51668 | biostudies-arrayexpress
Project description:White fin ornamentation in teleosts provides a striking model to study pigment cell diversity, differentiation, and patterning. In zebrafish (Danio rerio), white melanoleucophores (ML) and xantholeucophores (XL) produce white and yellowish-white fin patterns, respectively, arising from melanophore and xanthophore lineages. Here, we investigated white fin-pattern cells in zebrafish and a closely related cyprinid, the white cloud minnow (Tanichthys albonubes), which diverged 32–52 million years ago. We identified three distinct leucophore phenotypes in cyprinids: ML, XL, and Tanichthys leucophores, the latter containing white material but lacking substantial carotenoid pigmentation. Transmission electron microscopy revealed that XL and Tanichthys leucophores contain large pterinosome-like organelles, distinct from melanoleucophores and iridophores, suggesting different physicochemical bases for these white phenotypes. Fate-mapping in zebrafish demonstrated that XL arise directly from xanthophore-like progenitors, a process dependent on gap-junction-mediated communication via Gja5b and Cx39.4. Bulk mRNA sequencing of XL versus progenitor cells revealed upregulation of pteridine biosynthesis genes, notably sepiapterin reductase (spra), whose disruption via CRISPR/Cas9 abrogated white pigment formation in both zebrafish XL and Tanichthys leucophores. Chemical analyses confirmed enrichment of colorless pteridines, including biopterin and pterin, in tissues containing these cells. Together, our findings demonstrate that convergent white fin patterns in zebrafish and white cloud minnow rely on pteridine-based leucophores, arising via lineage-specific differentiation programs, and underscore the diversity of cellular and molecular strategies underlying white pigmentation in cyprinids.
2026-03-05 | GSE313210 | GEO
Project description:Whole genome sequencing of White-backed and Hooded Vultures Van der Meer, K.A. & Ottenburghs, J. (expected mid 2024)
| PRJEB65321 | ENA
Project description:Purpose: To investigate the involvement of mTORC1 as a mediator of the actions of the PPARγ ligand rosiglitazone in subcutaneous inguinal white adipose tissue transcriptome; Methods: Mice bearing regulatory associated protein of mTOR (Raptor) deletion and therefore mTORC1 deficiency exclusively in adipocytes (adiponectin Cre recombinase) and littermate controls were fed a high-fat diet supplemented or not with the PPARγ agonist rosiglitazone (30 mg/kg/day) for 8 weeks and evaluated for inguinal white adipose tissue transcriptome (Rnaseq); Results: 3,2425 genes had their correspondent mRNA levels altered by either adipocyte Raptor deficiency or rosiglitazone administration or their combination. Among those, 408 genes modulated by rosiglitazone required mTORC1. Conclusion: PPARγ and mTORC1 are essential partners in the regulation of a cluster of genes in inguinal white adipose tissue.
2022-02-01 | GSE166988 | GEO