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202 results for “mutagenesis”
Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release
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Sequence Data for Templated Mutagenesis Analysis
<p>This repository contains the sequence data required for the analysis of templated mutagenesis.</p> <p>The sequences in the ebola folder are described in Bornholdt et al., "Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak" (dx.doi.org/10.1126/science.aad5788). The associated SRA accession numbers are listed in ebola/ebola_accessions_heavy.txt.</p> <p>The sequences in the yeap folder are described in Yeap et al., "Sequence-Intrinsic Mechanisms that Target AID<br> Mutational Outcomes on Antibody Genes" (http://dx.doi.org/10.1016/j.cell.2015.10.042). The associated SRA accession numbers are listed in yeap/SRR_Acc_List_gpt.txt.</p> <p>The sequences in the reference_sets folder are derived from IMGT (http://www.imgt.org/vquest/refseqh.html) and Retter et al., "Sequence and Characterization of the Ig Heavy Chain Constant and Partial Variable Region of the Mouse Strain 129S1" (https://doi.org/10.4049/jimmunol.179.4.2419). More information about how the sequences were accessed and processed is available in reference_sets/README.md.</p>
Data from: CRISPR/cas9-mediated targeted mutagenesis for functional genomics research of Crassulacean acid metabolism plants
Crassulacean acid metabolism (CAM) is an important photosynthetic pathway in diverse lineages of plants featuring high water-use efficiency and drought tolerance. A big challenge facing the CAM research community is to understand the function of the annotated genes in CAM plant genomes. Recently, a new genome editing technology using CRISPR/Cas9 has become a more precise and powerful tool than traditional approaches for functional genomics research in C3 and C4 plants. In this study, we seek to realize the potential of CRISPR/Cas9 to characterize the function of CAM-related genes in the model CAM species Kalanchoë fedtschenkoi. We demonstrate that CRISPR/Cas9 is effective to create biallelic indel mutagenesis to reveal previously unknown roles of blue light receptor phototropin 2 (KfePHOT2) in the CAM pathway. Knocking-out of the KfePHOT2 reduced stomatal conductance and CO2 fixation in the late afternoon and increased stomatal conductance and CO2 fixation in the early evening, indicating that blue light signaling plays an important role in the CAM pathway. Lastly, we provide a genome-wide gRNA database targeting 45,183 protein-coding genes annotated in the K. fedtschenkoi genome.
Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis
Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.
Data from: In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool
Chemical hazard assessment requires extrapolation of information from model organisms to all species of concern. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed as a rapid, cost effective method to aid cross-species extrapolation of susceptibility to chemicals acting on specific protein targets through evaluation of protein structural similarities and differences. The greatest resolution for extrapolation of chemical susceptibility across species involves comparisons of individual amino acid residues at key positions involved in protein-chemical interactions. However, a lack of understanding of whether specific amino acid substitutions among species at key positions in proteins affect interaction with chemicals made manual interpretation of alignments time consuming and potentially inconsistent. Therefore, this study used in silico site-directed mutagenesis coupled with docking simulations of computational models for acetylcholinesterase (AChE) and ecdysone receptor (EcR) to investigate how specific amino acid substitutions impact protein-chemical interaction. This study found that computationally derived substitutions in identities of key amino acids caused no change in protein-chemical interaction if residues share the same side chain functional properties and have comparable molecular dimensions, while differences in these characteristics can change protein-chemical interaction. These findings were considered in the development of capabilities for automatically generated species-specific predictions of chemical susceptibility in SeqAPASS. These predictions for AChE and EcR were shown to agree with SeqAPASS predictions comparing the primary sequence and functional domain sequence of proteins for more than 90 % of the investigated species, but also identified dramatic species-specific differences in chemical susceptibility that align with results from standard toxicity tests. These results provide a compelling line-of-evidence for use of SeqAPASS in deriving screening level, species-specific, susceptibility predictions across broad taxonomic groups for application to human and ecological hazard assessment.
Data from: Forward genetic screening for regulators involved in cholesterol synthesis using validation-based insertional mutagenesis
Somatic cell genetics is a powerful approach for unraveling the regulatory mechanism of cholesterol metabolism. However, it is difficult to identify the mutant gene(s) due to cells are usually mutagenized chemically or physically. To identify important genes controlling cholesterol biosynthesis, an unbiased forward genetics approach named validation-based insertional mutagenesis (VBIM) system was used to isolate and characterize the 25-hydroxycholesterol (25-HC)-resistant and SR-12813-resisitant mutants. Here we report that five mutant cell lines were isolated. Among which, four sterol-resistant mutants either contain a truncated NH2-terminal domain of sterol regulatory element-binding protein (SREBP)-2 terminating at amino acids (aa) 400, or harbor an overexpressed SREBP cleavage-activating protein (SCAP). Besides, one SR-12813 resistant mutant was identified to contain a truncated COOH-terminal catalytic domain of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase). This study demonstrates that the VBIM system can be a powerful tool to screen novel regulatory genes in cholesterol biosynthesis.
Data from: Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis
Populations may genetically adapt to severe stress that would otherwise cause their extirpation. Recent theoretical work, combining stochastic demography with Fisher's Geometric Model of adaptation, has shown how evolutionary rescue becomes unlikely beyond some critical intensity of stress. Increasing mutation rates may however allow adaptation to more intense stress, raising concerns about the effectiveness of treatments against pathogens. This previous work assumes that populations are rescued by the rise of a single resistance mutation. However, even in asexual organisms, rescue can also stem from the accumulation of multiple mutations in a single genome. Here, we extend this model to study the rescue process in an asexual population where the mutation rate is sufficiently high so that such events may be common. We predict both the ultimate extinction probability of the population and the distribution of extinction times. We compare the accuracy of different approximations covering a large range of mutation rates. Moderate increase in mutation rates favors evolutionary rescue. However, larger increase leads to extinction by the accumulation of a large mutation load, a process called lethal mutagenesis. We discuss how these results could help design "evolution-proof" anti-pathogen treatments that even highly mutable strains could not overcome.
Data from: Evolution of stress-induced mutagenesis in the presence of horizontal gene transfer
Stress-induced mutagenesis has been observed in multiple species of bacteria and yeast. It has been suggested that in asexual populations, a mutator allele that increases the mutation rate during stress can sweep to fixation with the beneficial mutations it generates. However, even asexual microbes can undergo horizontal gene transfer and rare recombination, which typically interfere with the spread of mutator alleles. Here we examine the effect of horizontal gene transfer on the evolutionary advantage of stress-induced mutator alleles. Our results demonstrate that stress-induced mutator alleles are favored by selection even in the presence of horizontal gene transfer, and more so when the mutator alleles also increase the horizontal gene transfer rate. We suggest that when regulated by stress, mutation and horizontal gene transfer can be complementary, rather than competing, adaptive strategies, and that stress-induced mutagenesis has important implications for evolutionary biology, ecology, and epidemiology, even in the presence of horizontal gene transfer and rare recombination.
Restraints based on mutagenesis data
<p>Restraints generated by HADDOCK based on a mutational mapping of the Rev7 dimer interface.</p>
Fig. 5 in Mutagenesis of a Lotus japonicus GSK3β/Shaggy-like kinase reveals functionally conserved regulatory residues
Fig. 5. The enzymatic activity of native LjSK1. The inset shows the Lineweaver- Burk plot.
Fig. 6 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 6. Hydroxylated sesquiterpene product of PmSTS mutants L454G and L454A.
Data from: In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool
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Data from: Stress-induced mutagenesis and complex adaptation
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Data from: Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis
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Data from: CRISPR/cas9-mediated targeted mutagenesis for functional genomics research of Crassulacean acid metabolism plants
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Data from: Evolution of stress-induced mutagenesis in the presence of horizontal gene transfer
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Data from: CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing
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Data from: Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis
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Data from: Forward genetic screening for regulators involved in cholesterol synthesis using validation-based insertional mutagenesis
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Lentiviral-based mutagenesis to identify mutations that confer resistance to anti-cancer drugs
GEO Series GSE164664. Homo sapiens. 145 samples. Type: Other; Expression profiling by high throughput sequencing.
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Allen Brain Atlas
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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.
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