Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1189165 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations.
2010-11-30 | GSE22494 | GEO
Project description:Monkeypox virus (MPXV) is a zoonotic virus endemic to Africa that has recently re-emerged, becoming the first orthopoxvirus with sustained human-to-human transmission since smallpox eradication. The 2022 global epidemic of MPXV was caused by Clade IIb virus (lineage B.1) that derived from the lineage A endemic to West Africa through APOBEC3 microevolution1-3. Here, comparison of lineage B.1 virus with its closest earlier A.1 ancestor reveals that despite only 46 nucleotide differences, lineage B.1 has attenuating phenotypic changes. Both viruses replicated equivalently in cell culture, but B.1 had defects in long-range spread, which mapped to APOBEC3 mutation E353K in OPG057 (F13L). MPXV B.1 was also defective in innate immune control, inducing higher IFNβ and innate immune signalling gene expression, and showing reduced capacity to suppress interleukin-1β-mediated responses, which mapped to APOBEC mutation R48C in OPG047 (F3L). Finally, MPXV B.1 had reduced virulence in a mouse model of MPXV infection relative to the ancestral A.1 strain. Our work demonstrates that the 2022 global outbreak MPXV was intrinsically attenuated, with attenuating mutations that are absent in concurrent, more severe clade IIb outbreaks. Our data also reveal that APOBEC3 editing is a mechanism of MPXV phenotypic variation, potentially contributing to clade evolution and competition.
2026-07-15 | GSE338258 | GEO
Project description:Array CGH analysis of Helicobacter pylori strains isolated from a North American cohort of symptomatic pediatric patients. Keywords: genotyping_design
2009-11-05 | GSE13317 | GEO
Project description:Legumes have evolved lineage-specific peptides to control rhizobia and sustain nitrogen fixation. In inverted repeat-lacking clade (IRLC) legumes, nodule-specific cysteine-rich (NCR) peptides enforce terminal bacteroid differentiation, maximizing symbiotic output but restricting nodule lifespan. By contrast, Robinioid legumes, the IRLC’s sister clade, lack NCRs yet yet include perennial species that maintain productive nodules for decades. Here we identify a nodule-proline-glycine-rich peptide family (NPGs) as a conserved, genus-wide innovation of Robinia. NPGs are highly abundant, localize to the symbiosome membrane, and are intrinsically disordered. Exposure of Mesorhizobium robiniae to recombinant NPGs reprograms physiology, inducing nitrogenase expression while dampening growth without loss of viability. NPGs thus exemplify a distinct, reversible strategy of symbiont control, expanding the peptide repertoire that supports nitrogen fixation in perennial legumes.
2026-05-06 | GSE307061 | GEO
Project description:Legumes have evolved lineage-specific peptides to control rhizobia and sustain nitrogen fixation. In inverted repeat-lacking clade (IRLC) legumes, nodule-specific cysteine-rich (NCR) peptides enforce terminal bacteroid differentiation, maximizing symbiotic output but restricting nodule lifespan. By contrast, Robinioid legumes, the IRLC’s sister clade, lack NCRs yet yet include perennial species that maintain productive nodules for decades. Here we identify a nodule-proline-glycine-rich peptide family (NPGs) as a conserved, genus-wide innovation of Robinia. NPGs are highly abundant, localize to the symbiosome membrane, and are intrinsically disordered. Exposure of Mesorhizobium robiniae to recombinant NPGs reprograms physiology, inducing nitrogenase expression while dampening growth without loss of viability. NPGs thus exemplify a distinct, reversible strategy of symbiont control, expanding the peptide repertoire that supports nitrogen fixation in perennial legumes.
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Project description:Purpose: The goal of the current study was to find the candidate genes responsible for the habita specific clock variation in N. discreta. Methods: We performed RNA-seq experiment using four strains ; African parent (FGSC8831), North American parent (FGSC 8578) and two representative progeny representing African clock phenotype (N309-89) and North American clock phenotype (N309-50). Results: We identified one candidate gene that meets our criteria; confirmed it's expression by qPCR and it's expression pattern is associated with parent genotype. Conclusions: Our approach using the expression profiles and SNP data of two parents and two representative progeny led us to identify a candidate gene for a complex clock adaptation phenotype.
2018-09-18 | GSE120053 | GEO
Project description:The goal of the study was to test whether CBD103 genotype of North American gray wolves impacts the gene expression response to polyI:C or to live canine distemper virus. We established 24 primary cultures of epidermal keratinocytes from skin punches of North American gray wolves, and also generated an immortalized keratinocyte line and a CRISPR/Cas9 edited cell line. We evaluated the gene expression response of cells to either 24 hours challenge with 1 ug/ml polyI:C or to five days challenge with live canine distemper virus (100 TCID50/ml). Every challenged cell culture had a paired null control sample (plated and collected at same time points).
2021-05-06 | GSE163163 | GEO