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1,023 results for “copy number”
A streamlined approach for fluorescence labelling of low copy-number plasmids for determination of conjugation frequency by flow cytometry
<p><span>Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. </span>Robust <span>measurement</span> of<span> the conjugation frequency of plasmids between bacterial strains and species </span>is therefore important <span>to understand the transfer dynamics </span>and epidemiology <span>of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescence gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. </span><span>A small non-conjugative plasmid, which carries a red fluorescence gene with a toxin-antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescence gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescence genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time. </span></p>
Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen - Supplementary Tables..
<p>Supplementary Tables S1 - S11 of the manuscript <strong>Copy number variation introduced by a massive mobile element underpins global thermal adaptation in a fungal wheat pathogen. </strong></p>
A streamlined approach for fluorescence labelling of low copy-number plasmids for determination of conjugation frequency by flow cytometry
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Data from: Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients
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Data from: Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers, and life history
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Data from: The fire ant social supergene is characterized by extensive gene and transposable element copy number variation
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Accumulation of gene copy number variations during the early phase of free-spawning abalone speciation
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Data from: The effect of copy number hemiplasy on gene family evolution
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Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy
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Data from: Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
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Data from: Higher evolutionary dynamics of gene copy number for Drosophila glue genes located near short repeat sequences
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Amaranthus palmeri EPSPS copy number and glyphosate resistance variation
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Convergent evolution and predictability of gene copy numbers associated with diets in mammals
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Somatic copy number and structural variation in RPE-1 cells with induced chromosomal instability
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Data from: Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab
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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
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Avian MHC copy number variation is associated with helminth richness
<p>Genes of the Major Histocompatibility Complex (MHC) play a key role in the adaptive immunity of vertebrates, as they encode receptors responsible for recognition of antigens. Evolutionary history of the MHC proceeded through numerous gene duplications, which increases the spectrum of pathogens recognized by individuals. Although pathogen-mediated selection is believed to be a primary driver of MHC expansion over evolutionary times, empirical evidence for this association is virtually lacking. Here, we used an extensive dataset on MHC class II copy number variation in non-passerine birds to test for an evolutionary correlation with helminth parasite richness. As expected, our phylogenetically-informed modelling revealed a positive association between MHC copy number and total helminth richness, even after controlling for a broad spectrum of ecological and life-history traits. Thus, total helminth richness appears to be the most important correlate of MHC copy number, supporting a leading role of pathogen-mediated selection in the evolution of MHC in birds. Our results provide some of the first, although correlative, evidence linking parasitism to inter-specific variation in MHC copy number among birds.</p>
NanoString nCounter copy number variation assay
<p>The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited Y and W chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies, and the W chromosome has been largely overlooked. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the W both across and within avian species. We find a striking deficit of gene families on the duck W chromosome, as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Furthermore, we show that gene families have expanded independently in the duck and chicken. In particular, using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors, we investigate the factors driving the expansion of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. While we find that HINTW is ampliconic in both species, our results support a role of female-specific selection in driving gene amplification in the chicken but not the duck, challenging the assumption that HINTW is key for female fecundity across the avian phylogeny.</p>
Paternally inherited P-element copy number affects the magnitude of hybrid dysgenesis in Drosophila simulans and D. melanogaster
<p class="CxSpFirst">Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. <i>P</i>-elements (PEs) in <i>Drosophila</i> are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short and long-read sequenced to infer the number of PEs in the genomes of dozens of isofemale lines from two <i>Drosophila</i> species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M ´ ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species which suggest there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species-specific.</p>
Data from: Distribution and functionality of copy number variation across European cattle populations
Copy number variation (CNV), which is characterized by large-scale losses or gains of DNA fragments, contributes significantly to genetic and phenotypic variation. Assessing CNV across different European cattle populations might reveal genetic changes responsible for phenotypic differences, which have accumulated throughout the domestication history of cattle as consequences of evolutionary forces that act upon them. To explore pattern of CNVs across European cattle, we genotyped 149 individuals, that represent different European regions, using the Illumina Bovine HD Genotyping array. A total of 9,944 autosomal CNVs were identified in 149 samples using a Hidden Markov Model (HMM) as employed in PennCNV. Animals originating from several breeds of British Isles, and Balkan and Italian regions, on average, displayed higher abundance of CNV counts than Dutch or Alpine animals. A total of 923 CNV regions (CNVRs) were identified by aggregating CNVs overlapping in at least two animals. The hierarchical clustering of CNVRs indicated low differentiation and sharing of high-frequency CNVRs between European cattle populations. Various CNVRs identified in the present study overlapped with olfactory receptor genes and genes related to immune system. In addition, we also detected a CNV overlapping the Kit gene in English longhorn cattle which has previously been associated with color-sidedness. To conclude, we provide a comprehensive overview of CNV distribution in genome of European cattle. Our results indicate an important role of purifying selection and genomic drift in shaping CNV diversity that exists between different European cattle populations.
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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)
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DANDI Archive for NWB datasets
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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.