Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
39
datasets available to search
ShareScore release 0.9.0
Dataset results
39 results for “spontaneous mutation”
Characterization of cefiderocol resistant spontaneous mutant variants of Klebsiella pneumoniae producing NDM-5 with single mutation in cirA
<p>Cefiderocol (CFDC) is a siderophore-cephalosporin antibiotic designed to combat highly resistant Gram-negative bacterial infections. Its mechanism involves a strong affinity for iron and active transport into bacterial cells, providing an alternative against strains resistant to common antibiotics. However, the emergence of CFDC resistance in Klebsiella is a growing concern. Recent reports highlight increasing CFDC resistance in K. pneumoniae, particularly associated with mutations in the cirA gene, responsible for encoding a siderophore receptor. Co-localization of blaNDM-like gene and cirA mutations correlates with higher CFDC resistance. The study focuses on a carbapenem-resistant K. pneumoniae strain (Kp-1) with carbapenemases blaNDM-5 and blaOXA-181, recovered from a post-surgery patient. The strain exhibited resistance to all tested antibiotics but susceptibility to CFDC. Heteroresistant populations with the halo on inhibition of CFDC were observed. Genomic analysis identified a novel mutation (W123*) in the cirA gene associated with CFDC resistance. Additionally, increased blaNDM-5 expression in Kp-1 IHC (intra-halo colony) compared to Kp-1 was noted. The coexistence of blaNDM-like and cirA variants, along with high blaNDM-5 expression, explains the observed 21-fold increase in Minimum Inhibition Concentration (MIC) in Kp-1 IHC. The study contributes to understanding the molecular mechanisms driving the emergence of cefiderocol resistance, emphasizing the significance of coexisting mutations in cirA and blaNDM-like genes.</p>
Epigenetic modifications modify the rate of spontaneous mutations in a pathogenic fungus
<p>Mutations are the source of genetic variation and the substrate for evolution. Genome-wide mutation rates appear to be affected by selection and are probably adaptive. Mutation rates are also known to vary along genomes, possibly in response to epigenetic modifications, but causality is only assumed. In this study we determine the direct impact of epigenetic modifications and temperature stress on mitotic mutation rates in a fungal pathogen using a mutation accumulation approach. Deletion mutants lacking epigenetic modifications confirm that histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate. Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate 15‑fold resulting in significantly less TE mobilization. Also accessory chromosomes have significantly higher mutation rates. Finally, we find that temperature stress substantially elevates the mutation rate. Taken together, we find that epigenetic modifications and environmental conditions modify the rate and the location of spontaneous mutations in the genome and alter its evolutionary trajectory.</p>
On ageing and age-specific effects of spontaneous mutations
<p>Evolutionary theories of ageing assume causal mutations either have beneficial early-life effects which gradually become deleterious with advancing age (antagonistic pleiotropy: AP) or mutations that only have deleterious effects at old age (mutation accumulation: MA). Mechanistically, ageing is predicted to result from damage accumulating in the soma. While this scenario is compatible with AP, it is not immediately obvious how damage would accumulate under MA. In a modified version of the MA theory, it has been suggested that mutations with weakly deleterious effects at young age can also contribute to ageing, if they generate damage that gradually accumulates with age. Mutations with increasing deleterious effects have recently gained support from theoretical work and studies of large-effect mutations. Here we address if spontaneous mutations also have negative effects that increase with age. We accumulate mutations with early-life effects in <em>Drosophila</em> <em>melanogaster</em> across 27 generations and compare their relative effects on fecundity early and late in life. Our mutation accumulation lines on average have substantially lower early-life fecundity compared to controls. These effects were further maintained throughout life, but they did not increase with age. Our results thus suggest that most spontaneous mutations do not contribute to damage accumulation and ageing.</p>
On ageing and age-specific effects of spontaneous mutations
Open the record for dataset details and reuse information.
Data required for "Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences"
<p>In the early 1900s,mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of NGS technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using next-generation sequencing (NGS) to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.</p>
Data from: Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana
As the ultimate source of genetic diversity, spontaneous mutation is critical to the evolutionary process. The fitness effects of spontaneous mutations are almost always studied under controlled laboratory conditions rather than under the evolutionarily relevant conditions of the field. Of particular interest is the conditionality of new mutations - i.e., is a new mutation harmful regardless of the environment in which it is found? In other words, what is the extent of genotype-environment interaction for spontaneous mutations? We studied the fitness effects of 25 generations of accumulated spontaneous mutations in Arabidopsis thaliana in two geographically widely separated field environments, in Michigan and Virginia. At both sites, mean total fitness of MA lines exceeded that of the ancestors, contrary to the expected decrease in the mean due to new mutations but in accord with prior work on these MA lines. We observed genotype-environment interactions in the fitness effects of new mutations, such that the effects of mutations in Michigan were a poor predictor of their effects in Virginia and vice versa. In particular, mutational variance for fitness was much larger in Virginia compared to Michigan. This strong genotype-environment interaction would increase the amount of genetic variation maintained by mutation-selection balance.
Data from: The contribution of spontaneous mutations to thermal sensitivity curve variation in Drosophila serrata
Many traits studied in ecology and evolutionary biology change their expression in response to a continuously varying environmental factor. One well-studied example are thermal performance curves (TPCs); continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding the trade-offs involved in thermal adaptation. We assayed TPCs for locomotor activity in a set of 66 spontaneous mutation accumulation lines in the fly Drosophila serrata. Factor-analytic modeling of the mutational variance-covariance matrix, M, revealed support for three axes of mutational variation in males and two in females. These independent axes of mutational variance corresponded well to the major axes of TPC variation required for different types of thermal adaptation; 'faster-slower' representing changes in performance largely independent of temperature, and the 'hotter-colder' and 'generalist-specialist' axes, representing trade-offs. In contrast to its near-absence from standing variance in this species, a 'faster-slower' axis, accounted for most mutational variance (75% in males and 66% in females) suggesting selection may easily fix or remove these types of mutations in outbred populations. Axes resembling the 'hotter-colder' and 'generalist-specialist' modes of variation contributed less mutational variance but nonetheless point to an appreciable input of new mutations that may contribute to thermal adaptation.
CarcSeq measurement of lung cancer driver mutations predicts mouse strain- and sex-related incidence of spontaneous lung neoplasia
<p>The data contained herein are the fastq files collected for individual mouse lung DNA samples. Ten samples each of male and female, B6C3F1 and CD-1 mouse lung DNA were analyzed using the CarcSeq method for error-corrected next-generation sequencing as previously described [Harris, KL, Walia, V, Gong, B, et al. Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq. <i>Environ Mol Mutagen</i>. 2020; 61: 872– 889. <a href="https://doi.org/10.1002/em.22409">https://doi.org/10.1002/em.22409</a> and Karen L McKim, Meagan B Myers, Kelly L Harris, Binsheng Gong, Joshua Xu, Barbara L Parsons, CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia, <em>Toxicological Sciences</em>, 2021;, kfab040, <a href="https://doi.org/10.1093/toxsci/kfab040">https://doi.org/10.1093/toxsci/kfab040</a>]. A readme text file provides the key to which sample numbers correspond with which mouse strain and sex. All the fastq files within a given folder were used to construct single strand consensus sequences, which were then subject to downstream analyses as reported in the associated publication.</p>
Data from: The contribution of spontaneous mutations to thermal sensitivity curve variation in Drosophila serrata
Open the record for dataset details and reuse information.
Data from: Field measurements of genotype by environment interaction for fitness caused by spontaneous mutations in Arabidopsis thaliana
Open the record for dataset details and reuse information.
Data from: Meiotic double strand DNA breaks and spontaneous mutation in <em>Drosophila melanogaster</em>
Open the record for dataset details and reuse information.
Data from: Fitness decline under osmotic stress in Caenorhabditis elegans populations subjected to spontaneous mutation accumulation at varying population sizes
Open the record for dataset details and reuse information.
Fitness effects of spontaneous mutation in a warming world
Open the record for dataset details and reuse information.
Data from: Fitness of Arabidopsis thaliana mutation accumulation lines whose spontaneous mutations are known
Open the record for dataset details and reuse information.
CarcSeq measurement of lung cancer driver mutations predicts mouse strain- and sex-related incidence of spontaneous lung neoplasia
Open the record for dataset details and reuse information.
Data from: Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster
In populations with males and females, sexual selection may often represent a major component of overall selection. Sexual selection could act to eliminate deleterious alleles in concert with other forms of selection, thereby improving the fitness of sexual populations. Alternatively, the divergent reproductive strategies of the sexes could promote the maintenance of sexually-antagonistic variation, causing sexual populations to be less fit. The net impact of sexual selection on fitness is not well understood, due in part to limited data on the sex-specific effects of spontaneous mutations on total fitness. Using a set of mutation accumulation lines of Drosophila melanogaster, we found that mutations were deleterious in both sexes and had larger effects on fitness in males than in females. This pattern is expected to reduce the mutation load of sexual females and promote the maintenance of sexual reproduction.
Data from: Abiotic stress does not magnify the deleterious effects of spontaneous mutations
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between fitness categories (high-fitness MA, low-fitness MA). If the environment and mutation load have synergistic effects on trait means, then the difference between the high and low-fitness MA lines should be larger in stressful environments. Although the stress treatments consistently decreased survival and/or viability, we did not detect significant interactions between fitness categories and environment types. In contrast, we did find consistent evidence for synergistic effects on (micro)environmental variation. The lack of signal in trait means likely reflects the very low starting fitness of some low-fitness MA lines, the potential for cross-stress responses and the context dependence of mutational effects. In addition, the large increases in the environmental variance in the stressful environments may have masked small changes in trait means. These results do not provide evidence for synergism between mutation and stress.
Data from: The rate and effects of spontaneous mutation on fitness traits in the social amoeba, Dictyostelium discoideum
We performed a mutation accumulation (MA) experiment using the social amoeba Dictyostelium discoideum to estimate the rate and distribution of effects of spontaneous mutations affecting eight putative fitness traits. We found that the per generation mutation rate for most fitness components is 0.0019 mutations per haploid genome per generation, or larger. This rate is an order of magnitude higher than estimates for fitness components in the unicellular eukaryote Saccharomyces cerevisiae, even though the base-pair substitution rate is two orders of magnitude lower. The high rate of fitness-altering mutations observed in this species may be partially explained by a large mutational target relative to Saccharomyces cerevisiae. Also, fitness-altering mutations may occur primarily at simple sequence repeats, which are common throughout the genome, including in coding regions, and may represent a target that is particularly likely to give fitness effects upon mutation. The majority of mutations had deleterious effects on fitness, but there was evidence for a substantial fraction, up to 40%, being beneficial for some of the putative fitness traits. Competitive ability within the multicellular slug appears to be under weak directional selection, perhaps reflecting the fact that slugs are sometimes, but not often, comprised of multiple clones in nature. Evidence for pleiotropy among fitness components across MA lines was absent, suggesting that mutations tend to act on single fitness components.
Data from: Fitness decline in spontaneous mutation accumulation lines of Caenorhabditis elegans with varying effective population sizes
The rate and fitness effects of new mutations have been investigated by mutation accumulation (MA) experiments in which organisms are maintained at a constant minimal population size to facilitate the accumulation of mutations with minimal efficacy of selection. We evolved 35 MA lines of Caenorhabditis elegans in parallel for 409 generations at three population sizes (N = 1, 10, and 100), representing the first spontaneous long-term MA experiment at varying population sizes with corresponding differences in the efficacy of selection. Productivity and survivorship in the N = 1 lines declined by 44% and 12%, respectively. The average effects of deleterious mutations in N = 1 lines are estimated to be 16.4% for productivity and 11.8% for survivorship. Larger populations (N = 10 and 100) did not suffer a significant decline in fitness traits despite a lengthy and sustained regime of consecutive bottlenecks exceeding 400 generations. Together, these results suggest that fitness decline in very small populations is dominated by mutations with large deleterious effects. It is possible that the MA lines at larger population sizes contain a load of cryptic deleterious mutations of small to moderate effects that would be revealed in more challenging environments.
Data from: Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
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)
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.