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38 results for “reverse genetics”
Data from: Dominance reversals and the maintenance of genetic variation
<p>Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (<em>e.g.</em> habitat, developmental stage, trait, or sex) being dominant in that context but recessive where deleterious. This context-dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods (dominance ordination, allele-specific expression, and allele-specific ATAC-Seq) that could facilitate the identification of antagonistic genetic variation. There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.</p>
Data from: Dominance reversals and the maintenance of genetic variation
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Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses
<p>This dataset contains data files and analysis code associated with manuscript entitled "Parallel reverse genetic screening in mutant human cells using transcriptomics".</p> <p>Data files include expression profiles for over 1800 RNA-seq samples and annotations.</p> <p>Analysis files include R scripts to generate summary figures.</p>
Reverse Genetic H9N2 Influenza Vaccine Study in Adults
ClinicalTrials.gov study NCT01320696. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Rapid reversal of a potentially constraining genetic covariance between leaf and flower traits in Silene latifolia
Genetic covariance between two traits generates correlated responses to selection, and may either enhance or constrain adaptation. Silene latifolia exhibits potentially constraining genetic covariance between specific leaf area and flower number in males. Flower number is likely to increase via fecundity selection but the correlated increase in specific leaf area increases mortality, and specific leaf area is under selection to decrease in dry habitats. We selected on trait combinations in two selection lines for four generations to test whether genetic covariance could be reduced without significantly altering trait means. In one selection line, the genetic covariance changed sign and eigenstructure changed significantly, while in the other selection line eigenstructure remained similar to the control line. Changes in genetic variance-covariance structure are therefore possible without the introduction of new alleles, and the responses we observed suggest that founder effects and changes in frequency of alleles of major effect may be acting to produce the changes.
Data from: Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation
Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the salt-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions.
Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus
Reverse genetic tools are essential for characterizing phenotypes of novel genes and testing functional hypotheses generated from next-generation sequencing studies. RNA interference (RNAi) has been a widely used technique for describing or quantifying physiological, developmental or behavioural roles of target genes by suppressing their expression. The marine intertidal copepod Tigriopus californicus has become an emerging model for evolutionary and physiological studies, but this species is not amenable to most genetic manipulation approaches. As crustaceans are susceptible to RNAi-mediated gene knock-down, we developed a simple method for delivery of gene-specific double-stranded RNA that results in significant suppression of target gene transcription levels. The protocol was examined on five genes of interest, and for each, at least 50% knock-down in expression was achieved. While knock-down levels did not reach 100% in any trial, a well-controlled experiment with one heat-shock gene showed unambiguously that such partial gene suppression may cause dramatic changes in phenotype. Copepods with suppressed expression of heat-shock protein beta 1 (hspb1) exhibited dramatically decreased tolerance to high temperatures, validating the importance of this gene during thermal stress, as proposed by a previous study. The application of this RNAi protocol in T. californicus will be invaluable for examining the role of genes putatively involved in reproductive isolation, mitochondrial function and local adaptation.
Supplementary Figure S3 The leave-one-out analysis of the association between insomnia and MetS components genetically in the reverse MR analysis.
<p>This figure described the leave-one-out analysis of the association between insomnia and MetS components genetically in the reverse MR analysis.</p>
Supplementary Figure S2.The funnel plots of the association between insomnia and MetS components genetically in the reverse MR analysis.
<p>This figure described the funnel plots of the association between insomnia and MetS components genetically in the reverse MR analysis.</p>
Steady-state and time-resolved data for the article "Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222"
<p>1. Steady-state data</p> <p>Spectra were taken with/without continuous irradiation with a wavelength of 450 nm.</p> <p>1.1 CNF absorption region (2200-2260 cm<sup>-1</sup>)</p> <p>1.2. Amide absorption region (1500-1800 cm<sup>-1</sup>)</p> <p>1.3. UV/Visible absorption region (320-550 nm)</p> <p>Each spectral region has 3 datasets:</p> <p>- DARK</p> <p>- LIT (photostationary state)</p> <p>- DIFFERENCE (lit-minus-dark)</p> <p>The first row contains the variants.</p> <p>The first column contains the wavenumber (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>2. Time-resolved data.</p> <p>Dark recovery reaction after switching lights off (wavelength of 450 nm).</p> <p>2.1. EL222_WT_H2O</p> <p>2.2. EL222_WT_D2O</p> <p>2.3. EL222_W31CNF</p> <p>2.4. EL222_L35CNF</p> <p>2.5. EL222_N53CNF</p> <p>2.6. EL222_Y136CNF</p> <p>2.7. EL222_M151CNF</p> <p>2.8. EL222_L216CNF</p> <p>2.9. EL222_LOV_H2O</p> <p>2.10. EL222_LOV_D2O</p> <p>For each variant we have measured 3 spectral regions (except for 2.1, 2.2., 2.9 and 2.10, which lack CNF):</p> <p>- CNF: 2200-2270 cm<sup>-1</sup></p> <p>- AMIDE: 1500-1750 cm<sup>-1</sup></p> <p>- UVVIS: 320-550 nm</p> <p>For each probe we have 2 datasets:</p> <p>- DATA: the experimental lit-minus-dark absorbance difference spectra. </p> <p>The first row contains the time delays (in seconds).</p> <p>The first column contains the wavenumbers (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>- LDA: the lifetime density maps calculated from the corresponding DATA using the inverse Laplace transform and maximum entropy penalty.</p> <p>The first row contains the lifetimes (in seconds).</p> <p>The first column contains the wavenumbers (in cm<sup>-1</sup>) or wavelength (in nm).</p> <p>If you use these datasets please cite:</p> <p>Chaudhari, A.S.; Chatterjee, A.; Domingos, C.A.O.: Andrikopoulos, P. C.; Liu, Y.; Andersson, I.; Schneider, B.; Lórenz-Fonfría, V.A.; Fuertes, G. Genetically Encoded Non-canonical Amino Acids Reveal Asynchronous Dark Reversion of Chromophore, Backbone and Side-chains in EL222. <em>Protein Science</em>. 2023 <a href="https://doi.org/10.1002/pro.4590">https://doi.org/10.1002/pro.4590</a></p>
Study of ALS Reversals 2: Genetic Analyses
ClinicalTrials.gov study NCT03464903. IPD Sharing: YES. Countries: 1. Publications: 5.
Data from: Population genetic structure and direct observations reveal sex-reversed patterns of dispersal in a cooperative bird
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Data from: Reverse genetics in the tidepool: knockdown of target gene expression via RNA interference in the copepod Tigriopus californicus
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Data from: Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation
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Rapid reversal of a potentially constraining genetic covariance between leaf and flower traits in Silene latifolia
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Data from: New locus reveals the genetic architecture of sex reversal in the Chinese tongue sole (Cynoglossus semilaevis)
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Data from: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer
Previous genetic studies of extant planktonic foraminifera have provided evidence that the traditional, strictly morphological definition of species in these organisms underestimates their biodiversity. Here, we report the first case where this pattern is reversed. The modern (sub)tropical species plexus Globigerinoides sacculifer is characterized by large morphological variability, which has led to the proliferation of taxonomic names attributed to morphological end-members within the plexus. In order to clarify the taxonomic status of its morphotypes and to investigate the genetic connectivity among its currently partly disjunct (sub)tropical populations, we carried out a global survey of two ribosomal RNA regions (SSU and ITS-1) in all recent morphotypes of the plexus collected throughout (sub)tropical surface waters of the global ocean. Unexpectedly, we find an extremely reduced genetic variation within the plexus and no correlation between genetic and morphological divergence, suggesting taxonomical overinterpretation. The genetic homogeneity within the morphospecies is unexpected, considering its partly disjunct range in the (sub)tropical Atlantic and Indo-Pacific and its old age (early Miocene). A sequence variant in the rapidly evolving ITS-1 region indicates the existence of an exclusively Atlantic haplotype, which suggests an episode of relatively recent (last glacial) isolation, followed by subsequent resumption of unidirectional gene flow from the Indo-Pacific into the Atlantic. This is the first example in planktonic foraminifera where the morphological variability in a morphospecies exceeds its rDNA genetic variability. Such evidence for inconsistent scaling of morphological and genetic diversity in planktonic foraminifera could complicate the interpretation of evolutionary patterns in their fossil record.
Data from: Identification of genes important for cutaneous function revealed by a large scale reverse genetic screen in the mouse
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Data from: The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer
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A Quantitative, High-Throughput Reverse Genetic Screen Reveals Novel Connections Between pre-mRNA Splicing and 5’ and 3’ end Transcript Determinants
GEO Series GSE34330. Saccharomyces cerevisiae. 64 samples. Type: Expression profiling by array; Expression profiling by RT-PCR.
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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.