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66 results for “clonal populations”
Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations
Understanding how diversity emerges in a single niche is not fully understood. Rugged fitness landscapes and epistasis between beneficial mutations could explain coexistence amongst emerging lineages. To provide an experimental test of this notion, we investigated epistasis amongst four pleiotropic mutations in rpoS, mglD, malT and hfq present in two coexisting lineages that repeatedly fixed in experimental populations of Escherichia coli. The mutations were transferred into the ancestral background individually or in combination of double or triple alleles. The combined competitive fitness of two or three beneficial mutations from the same lineage was consistently lower than the sum of the competitive fitness of single mutants – a clear indication of negative epistasis within lineages. We also found sign epistasis (i.e. the combined fitness of two beneficial mutations lower than the ancestor), not only from two different lineages (i.e. hfq and rpoS) but also from the same lineage (i.e. mglD and malT). The sign epistasis between loci of different lineages indeed indicated a rugged fitness landscape, providing an epistatic explanation for the coexistence of distinct rpoS and hfq lineages in evolving populations. The negative and sign epistasis between beneficial mutations within the same lineage can further explain the order of mutation acquisition.
Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However: tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato-specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato-specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists.
Chromatograms: Rapid multilocus adaptation of clonal cabbage leaf curl virus populations to Arabidopsis thaliana
<p>Sei-0 and Col-0 <em>Arabidopsis thaliana </em>plants were inoculated with WT and mutant cabbage leaf curl virus and PCR amplicons targeting the Rep gene region were Sanger-sequenced, as documented (Hoyer et al. <a href="http://doi.org/10.1094/PBIOMES-12-21-0077-R">2022</a>).</p>
Data from: Clonal genetic structure and diversity in populations of an aquatic plant with combined versus separate sexes
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Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Open the record for dataset details and reuse information.
Data from: Epistatic interactions determine the mutational pathways and coexistence of lineages in clonal Escherichia coli populations
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DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: All_EMT6_BC5000]
GEO Series GSE210047. Mus musculus. 18 samples. Type: Other.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: CD8 NK depletion 4T1 BC5000]
GEO Series GSE210048. Mus musculus. 30 samples. Type: Other.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: IT_and_cont_4T1_BC5000]
GEO Series GSE210050. Mus musculus. 23 samples. Type: Other.
Clonal lineage tracing and transcriptomics of cortical progenitor populations reveal maintenance of differentiation potential.
GEO Series GSE283411. Mus musculus. 5 samples. Type: Other; Expression profiling by high throughput sequencing.
Clonal CD8+ T Cells Populate the Leptomeninges and Coordinate with Immune Cells in Human Degenerative Brain Diseases
GEO Series GSE288856. Homo sapiens. 113 samples. Type: Expression profiling by high throughput sequencing; Other.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: IT_and_cont_4T1_BC250000]
GEO Series GSE210051. synthetic construct; Mus musculus. 34 samples. Type: Other.
RNAseq of Individual 4T1 Clonal Populations
GEO Series GSE63180. Mus musculus. 54 samples. Type: Expression profiling by high throughput sequencing.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: WT_nude_and_NSG_4T1_BC250000]
GEO Series GSE210053. Mus musculus. 24 samples. Type: Other.
Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations
GEO Series GSE182685. Homo sapiens. 22 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
RNA-Seq expression profiling of clonal populations from the OCI-C5x patient-derived ovarian clear cell carcinoma cell line
GEO Series GSE123426. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [Bulk RNAseq]
GEO Series GSE210054. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: WT_nude_and_NSG_4T1_BC5000]
GEO Series GSE210052. Mus musculus. 20 samples. Type: Other.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [WGS of target clones]
GEO Series GSE210055. Mus musculus. 4 samples. Type: Other.
DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy [DNA barcodes: CD8_NK_depletion_4T1_BC5000_rpt]
GEO Series GSE210049. Mus musculus. 34 samples. Type: Other.
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.