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756 results for “immune genes”
Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift
<p>Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon <em>Procyon</em> <em>lotor</em> invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific SNP markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, i.e. – less genetically diverse invasive population from Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to a new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.</p>
Immune Landscape and Gene Function Analysis of Uveal Melanoma Based on Focal Adhesion-Related Gene Typing
<p><strong>Figure legend</strong><strong>s</strong></p> <p><strong>Figure 1 Identification of focal adhesion gene clusters and immune analysis</strong></p> <p>(A) Relative changes in the area under the CDF curve. (B) Consensus clustering results, K=3. (C) Survival curves of different clusters. (D) ssGSEA heatmap showing differences in immune infiltration between clusters. (E) Expression levels of immune checkpoints in different clusters. (F) Violin plots of immune scores, stromal scores, ESTIMATE scores, and tumor purity scores.</p> <p> </p> <p><strong>Figure 2 GSEA pathway enrichment analysis</strong></p> <p> </p> <p><strong>Figure 3 PPI network related to DEGs between cluster 2 and clusters 1 and 3 and HUB gene selection</strong></p> <p>(A) Selection of DEGs between cluster 2 and clusters 1 and 3. (B) PPI network of DEGs between clusters. (C) Intersection analysis of the top 20 HUB genes in the PPI network using five algorithms.</p> <p> </p> <p><strong>Figure 4 Functional analysis of HUB genes in the interaction network and construction of co-expression network</strong></p> <p>(A) Heatmap showing the expression of HUB genes in cluster 2 and clusters 1 and 3. (B) GO functional enrichment analysis of HUB genes. (C) KEGG pathway enrichment analysis of HUB genes. (D) Construction of the co-expression network of HUB genes and their co-expressed genes.</p> <p> </p> <p><strong>Figure 5 Survival curves of patients corresponding to HUB genes at high and low expression levels</strong></p> <p> </p> <p><strong>Figure 6 Exploration of the correlation between HUB genes and drug sensitivity through CellMiner database</strong></p> <p> </p>
Study of Gene Modified Immune Cells in Patients With Advanced Melanoma
ClinicalTrials.gov study NCT00910650. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift
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Data from: Microevolutionary selection dynamics acting on immune genes of the green veined white butterfly, Pieris napi
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Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
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AAV-mediated Inner ear gene delivery triggers mild host immune responses in the mammalian inner ear
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Quit bugging me: Phorid fly parasitoids affect expression of an immune gene in foraging fire ant workers
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Data for: Preliminary study based on methylation and transcriptome gene sequencing of lncRNAs and immune infiltration in hypopharyngeal carcinoma
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No evidence for single-copy immune-gene specific signals of selection in termites
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Data from: Contemporary evolution of the innate immune receptor gene TLR3 in an isolated vertebrate population
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Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity
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Relationships between immune gene expression and circulating cytokine levels in wild house mice
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Divergence in coding sequence and expression of different functional categories of immune genes between two wild rodent species
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Data from: Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids
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Data from: Single cell RNA-seq analysis reveals that prenatal arsenic exposure results in long-term, adverse effects on immune gene expression in response to Influenza A infection
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16S rRNA gene sequencing data from: Breastmilk IgG engages the neonatal immune system to instruct immune responses to gut antigens
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Data from: Habitat fragmentation differentially shapes neutral and immune gene variation in a tropical bird species
<p>Habitat fragmentation is a major cause of biodiversity loss, responsible for an alteration of intraspecific patterns of neutral genetic diversity and structure. Although neutral genetic variation can be informative for demographic inferences, it may be a poor predictor of adaptive genetic diversity and thus of the consequences of habitat fragmentation on selective evolutionary processes. In this context, we contrasted patterns of genetic diversity and structure of neutral loci (microsatellites) and immune genes (i.e., toll-like receptors) in an understorey bird species, the wedge-billed woodcreeper <i>Glyphorynchus spirurus</i>. The objectives were (1) to investigate forest fragmentation effects on population genetic diversity, (2) to disentangle the relative role of demography (genetic drift and migration) and selection, and (3) to assess whether immunogenetic patterns could be associated with variation of ectoparasite (i.e., ticks) pressures. Our results revealed an erosion of neutral genetic diversity and a substantial genetic differentiation among fragmented populations, resulting from a decrease in landscape connectivity and leading to the divergence of distinct genetic pools at a small spatial scale. Patterns of genetic diversity observed for TLR4 and TLR5 were concordant with neutral genetic patterns, whereas those observed for TLR3 and TLR21 were discordant. This result underlines that the dominant evolutionary force shaping immunogenetic diversity (genetic drift vs. selection) may be different depending on loci considered. Finally, tick prevalence was higher in fragmented environments. We discussed the hypothesis that pathogen selective pressures may contribute to maintain adaptive genetic diversity despite the negative demographic effect of habitat fragmentation on neutral genetic diversity.</p>
Data from: DNA methylation predicts immune gene expression in introduced house sparrows (Passer domesticus)
Populations undergoing range expansions are often faced with novel selective pressures, and to cope with such challenges, populations must either adapt quickly or exhibit phenotypic plasticity. This latter option allows for rapid phenotypic adjustments and persistence in novel environments, and thus could be advantageous at range‐edges. Our previous research on house sparrows in Kenya—a site of ongoing range expansion— and a growing literature suggests that invasion success is facilitated by epigenetic regulation of gene expression. Previously, we found (i) differences in the expression of a microbial surveillance gene (i.e. Toll‐like receptor 4—TLR4), and (ii) extensive variation in genome‐wide DNA methylation among house sparrows across Kenya. Here, our goal was to investigate whether these two observations are related, specifically whether DNA methylation within a target sequence upstream of the TLR4 transcription start site is associated with variation in TLR4 expression. We found that DNA methylation in the aforementioned region was quite variable among individuals, and variation at one CpG site predicted differences in TLR4 expression. Moreover, we found genetic variation within the same sequence upstream of the TLR4 exon, but this variation did not predict TLR4 expression. To our knowledge, this is the first study to demonstrate an association between DNA methylation and the expression of an ecologically relevant trait in a range‐expanding vertebrate.
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes
Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.