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Academic literature on the topic 'Mutation'

Author: Grafiati

Published: 4 June 2021

Last updated: 28 July 2024

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Journal articles on the topic "Mutation"

1

GARCÍA-DORADO, A., C. LÓPEZ-FANJUL, and A. CABALLERO. "Properties of spontaneous mutations affecting quantitative traits." Genetical Research 74, no. 3 (December 1999): 341–50. http://dx.doi.org/10.1017/s0016672399004206.

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Recent mutation accumulation results from invertebrate species suggest that mild deleterious mutation is far less frequent than previously thought, implying smaller expressed mutational loads. Although the rate (λ) and effect (s) of very slight deleterious mutation remain unknown, most mutational fitness decline would come from moderately deleterious mutation (s ≈ 0·2, λ ≈ 0·03), and this situation would not qualitatively change in harsh environments. Estimates of the average coefficient of dominance (h¯) of non-severe deleterious mutations are controversial. The typical value of h¯ = 0·4 can be questioned, and a lower estimate (about 0·1) is suggested. Estimated mutational parameters are remarkably alike for morphological and fitness component traits (excluding lethals), indicating low mutation rates and moderate mutational effects, with a distribution generally showing strong negative asymmetry and little leptokurtosis. New mutations showed considerable genotype–environment interaction. However, the mutational variance of fitness-component traits due to non-severe detrimental mutations did not increase with environmental harshness. For morphological traits, a class of predominantly additive mutations with no detectable effect on fitness and relatively small effect on the trait was identified. This should be close to that responsible for standing variation in natural populations.

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2

Ellis, Nathan A. "Mutation-causing mutations." Nature 381, no. 6578 (May 1996): 110–11. http://dx.doi.org/10.1038/381110a0.

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Matsutani, Taro, Yuki Ueno, Tsukasa Fukunaga, and Michiaki Hamada. "Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference." Bioinformatics 35, no. 22 (April 16, 2019): 4543–52. http://dx.doi.org/10.1093/bioinformatics/btz266.

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Abstract Motivation A cancer genome includes many mutations derived from various mutagens and mutational processes, leading to specific mutation patterns. It is known that each mutational process leads to characteristic mutations, and when a mutational process has preferences for mutations, this situation is called a ‘mutation signature.’ Identification of mutation signatures is an important task for elucidation of carcinogenic mechanisms. In previous studies, analyses with statistical approaches (e.g. non-negative matrix factorization and latent Dirichlet allocation) revealed a number of mutation signatures. Nonetheless, strictly speaking, these existing approaches employ an ad hoc method or incorrect approximation to estimate the number of mutation signatures, and the whole picture of mutation signatures is unclear. Results In this study, we present a novel method for estimating the number of mutation signatures—latent Dirichlet allocation with variational Bayes inference (VB-LDA)—where variational lower bounds are utilized for finding a plausible number of mutation patterns. In addition, we performed cluster analyses for estimated mutation signatures to extract novel mutation signatures that appear in multiple primary lesions. In a simulation with artificial data, we confirmed that our method estimated the correct number of mutation signatures. Furthermore, applying our method in combination with clustering procedures for real mutation data revealed many interesting mutation signatures that have not been previously reported. Availability and implementation All the predicted mutation signatures with clustering results are freely available at http://www.f.waseda.jp/mhamada/MS/index.html. All the C++ source code and python scripts utilized in this study can be downloaded on the Internet (https://github.com/qkirikigaku/MS_LDA). Supplementary information Supplementary data are available at Bioinformatics online.

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Lee, Joon-Hyop, Jiyoung Ahn, Won Seo Park, Eun Kyung Choe, Eunyoung Kim, Rumi Shin, Seung Chul Heo, et al. "Colorectal Cancer Prognosis is Not Associated with BRAF and KRAS Mutations-A STROBE Compliant Study." Journal of Clinical Medicine 8, no. 1 (January 17, 2019): 111. http://dx.doi.org/10.3390/jcm8010111.

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Background: We investigated the associations between v-Raf murine sarcoma viral oncogene homolog B1 (BRAFV600E, henceforth BRAF) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and colorectal cancer (CRC) prognosis, using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GSE39582) datasets. Materials and Methods: The effects of BRAF and KRAS mutations on overall survival (OS) and disease-free survival (DFS) of CRC were evaluated. Results: The mutational status of BRAF and KRAS genes was not associated with overall survival (OS) or DFS of the CRC patients drawn from the TCGA database. The 3-year OS and DFS rates of the BRAF mutation (+) vs. mutation (−) groups were 92.6% vs. 90.4% and 79.7% vs. 68.4%, respectively. The 3-year OS and DFS rates of the KRAS mutation (+) vs. mutation (−) groups were 90.4% vs. 90.5% and 65.3% vs. 73.5%, respectively. In stage II patients, however, the 3-year OS rate was lower in the BRAF mutation (+) group than in the mutation (−) group (85.5% vs. 97.7%, p <0.001). The mutational status of BRAF genes of 497 CRC patients drawn from the GSE39582 database was not associated with OS or DFS. The 3-year OS and DFS rates of BRAF mutation (+) vs. mutation (−) groups were 75.7% vs. 78.9% and 73.6% vs. 71.1%, respectively. However, KRAS mutational status had an effect on 3-year OS rate (71.9% mutation (+) vs. 83% mutation (−), p = 0.05) and DFS rate (66.3% mutation (+) vs. 74.6% mutation (−), p = 0.013). Conclusions: We found no consistent association between the mutational status of BRAF nor KRAS and the OS and DFS of CRC patients from the TCGA and GSE39582 databases. Studies with longer-term records and larger patient numbers may be necessary to expound the influence of BRAF and KRAS mutations on the outcomes of CRC.

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Bustamante, A. V., A. M. Sanso, D. O. Segura, A. E. Parma, and P. M. A. Lucchesi. "Dynamic of Mutational Events in Variable Number Tandem Repeats ofEscherichia coliO157:H7." BioMed Research International 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/390354.

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VNTRs regions have been successfully used for bacterial subtyping; however, the hypervariability in VNTR loci is problematic when trying to predict the relationships among isolates. Since few studies have examined the mutation rate of these markers, our aim was to estimate mutation rates of VNTRs specific for verotoxigenicE. coliO157:H7. The knowledge of VNTR mutational rates and the factors affecting them would make MLVA more effective for epidemiological or microbial forensic investigations. For this purpose, we analyzed nine loci performing parallel, serial passage experiments (PSPEs) on 9 O157:H7 strains. The combined 9 PSPE population rates for the 8 mutating loci ranged from 4.4 × 10−05to 1.8 × 10−03mutations/generation, and the combined 8-loci mutation rate was of 2.5 × 10−03mutations/generation. Mutations involved complete repeat units, with only one point mutation detected. A similar proportion between single and multiple repeat changes was detected. Of the 56 repeat mutations, 59% were insertions and 41% were deletions, and 72% of the mutation events corresponded to O157-10 locus. For alleles with up to 13 UR, a constant and low mutation rate was observed; meanwhile longer alleles were associated with higher and variable mutation rates. Our results are useful to interpret data from microevolution and population epidemiology studies and particularly point out that the inclusion or not of O157-10 locus or, alternatively, a differential weighting data according to the mutation rates of loci must be evaluated in relation with the objectives of the proposed study.

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Pawlik, Timothy M., Darrell R. Borger, Yuhree Kim, David Cosgrove, Sorin Alexandrescu, Ryan Thomas Groeschl, Vikram Deshpande, et al. "Genomic profiling of intrahepatic cholangiocarcinoma: Refining prognostic determinants and identifying therapeutic targets." Journal of Clinical Oncology 32, no. 3_suppl (January 20, 2014): 210. http://dx.doi.org/10.1200/jco.2014.32.3_suppl.210.

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210 Background: The molecular alterations that drive tumorigenesis in intrahepatic cholangiocarcinoma (ICC) remain poorly defined. We sought to define the incidence and prognostic significance of mutations associated with ICC among patients undergoing surgical resection. Methods: 138 patients who underwent resection at 6 centers in the United States and Europe were included in the cohort. Mutational profiling was performed using nucleic acids that were extracted from resected ICC tumor specimens; mutations were identified using a multiplexed mutational profiling platform. The frequency of mutations was ascertained and the impact on outcome determined. Results: Most patients had a solitary tumor (82%) and median tumor size was 6.0cm. Most patients had R0 resection (89%); 19% patients had N1 disease, while 15% had microscopic vascular invasion. A minority received adjuvant therapy (30%). The majority (55%) of patients had no genetic mutation identified. Among the 62 (45%) patients with a genetic mutation, only a small number of gene mutations were identified with a frequency of >5%: IDH1 (17.4%), KRAS (8.7%), BRAF (5.8%), PIK3CA (5.1%). In contrast, other genetic mutations were identified in very low frequency: IDH2 (3.6%), NRAS (3.6%), TP53 (2.2%), MAP2K1 (1.5%), CTNNB1 (0.7%), and PTEN (0.7%). Approximately 7% of IDH1-mutant tumors were associated with a concurrent PIK3CA gene mutation, and to a much lower extent, a mutation in MAP2K1 (2%). No concurrent mutations in IDH1 and KRAS were noted. Compared with ICC tumors that had no identified mutation, IDH1-mutant tumors were more often bilateral (OR 3.46), while KRAS-mutant tumors were more likely to be associated with perineural invasion (OR 5.72)(both P<0.05). While clinicopathological features such as tumor number and nodal status were associated with survival, no specific mutation was associated with prognosis. Conclusions: Most patients with resected ICC had no somatic mutation identified on multiplexed mutational profiling. IDH1 and KRAS were the most common mutations noted. While certain mutations were associated with ICC clinicopathological features, mutational status did not seemingly impact long-term prognosis.

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Robinson, Philip S., Tim H. H. Coorens, Claire Palles, Emily Mitchell, Federico Abascal, Sigurgeir Olafsson, Bernard C. H. Lee, et al. "Increased somatic mutation burdens in normal human cells due to defective DNA polymerases." Nature Genetics 53, no. 10 (September 30, 2021): 1434–42. http://dx.doi.org/10.1038/s41588-021-00930-y.

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AbstractMutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.

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Trindade, Sandra, Lilia Perfeito, and Isabel Gordo. "Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1544 (April 27, 2010): 1177–86. http://dx.doi.org/10.1098/rstb.2009.0287.

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Knowledge of the mutational parameters that affect the evolution of organisms is of key importance in understanding the evolution of several characteristics of many natural populations, including recombination and mutation rates. In this study, we estimated the rate and mean effect of spontaneous mutations that affect fitness in a mutator strain of Escherichia coli and review some of the estimation methods associated with mutation accumulation (MA) experiments. We performed an MA experiment where we followed the evolution of 50 independent mutator lines that were subjected to repeated bottlenecks of a single individual for approximately 1150 generations. From the decline in mean fitness and the increase in variance between lines, we estimated a minimum mutation rate to deleterious mutations of 0.005 (±0.001 with 95% confidence) and a maximum mean fitness effect per deleterious mutation of 0.03 (±0.01 with 95% confidence). We also show that any beneficial mutations that occur during the MA experiment have a small effect on the estimate of the rate and effect of deleterious mutations, unless their rate is extremely large. Extrapolating our results to the wild-type mutation rate, we find that our estimate of the mutational effects is slightly larger and the inferred deleterious mutation rate slightly lower than previous estimates obtained for non-mutator E. coli .

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Watters, M. K., and D. R. Stadler. "Spontaneous mutation during the sexual cycle of Neurospora crassa." Genetics 139, no. 1 (January 1, 1995): 137–45. http://dx.doi.org/10.1093/genetics/139.1.137.

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Abstract The DNA sequences of 42 spontaneous mutations of the mtr gene in Neurospora crassa have been determined. The mutants were selected among sexual spores to represent mutations arising in the sexual cycle. Three sexual-cycle-specific mutational classes are described: hotspot mutants, spontaneous repeat-induced point mutation (RIPs) and mutations occurring during a mutagenic phase of the sexual cycle. Together, these three sexual-cycle-specific mutational classes account for 50% of the mutations in the sexual-cycle mutational spectrum. One third of all mutations occurred at one of two mutational hotspots that predominantly produced tandem duplications of varying lengths with short repeats at their end-points. Neither of the two hotspots are present in the vegetative spectrum, suggesting that sexual-cycle-specific mutational pathways are responsible for their presence in the spectrum. One mutant was observed that appeared to have been RIPed precociously. The usual prerequisite for RIP, a duplication of the affected region, was not present in the parent stocks and was not detected in this mutant. Finally, there is a phase early in the premeiotic sexual cycle that is overrepresented in the generation of mutations. This "peak" appears to represent a phase during which the mutation rate rises significantly. This phase produces a disproportionally high fraction of frame shift mutations (3/6). In divisions subsequent to this, the mutation rate appears to be constant.

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Lee, Seung-Shin, Jae-Sook Ahn, Taehyung Kim, Hyeoung Joon Kim, Yeo-Kyeoung Kim, Seo-Yeon Ahn, Sung-Hoon Jung, et al. "RUNX1 Mutation in Cytogenetically Normal Acute Myeloid Leukemia : Clinical Implications, Co-Mutation Analysis." Blood 128, no. 22 (December 2, 2016): 5253. http://dx.doi.org/10.1182/blood.v128.22.5253.5253.

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Abstract Background and Objectives Acute Myeloid Leukemia (AML) is a cytogenetically and molecularly heterogeneous disease. In the recent decades, many genetic mutations and their clinical significances in AML have been identified with the development of new genomics technology. Based on these advances, new 2 entities were added to the WHO 2008 classification : AML with mutated NPM1 and AML with mutated CEBPA. Likewise, AML with RUNX1 mutation are now considered as a new provisional entity in the next update of WHO classification. In this work, we characterized patients with cytogenetically normal AML according to RUNX1 mutational status and analyzed several co-mutations by next generation sequencing. Patients and Methods A total of 419 patients were included in the present study who met the following eligibility criteria: 1) age ≥ 15 years; 2) a diagnosis of AML with normal karyotype confirmed by conventional cytogenetic analysis. Analysis of genetic mutations were performed using targeted resequencing by Illumina Hiseq 2000 (Sureselect custom probe set targeting 94 myeloid gene panel including RUNX1 mutation). Samples for the confirmation of first complete response were also analyzed in 163 patients. The majority of patients (97%) received '3+7' standard induction chemotherapy. Median age was 53(range 15-84). Results Overall, most common mutations for this cohort were NPM1(33.9%), DNMT3A(30.3%), NRAS(20.2%), IDH2(15.0%), FLT3(12.2%), CEBPA(11.1%). RUNX1 mutations were found in 22 of 419 (5.4%) patients. 7 of 13 available samples in complete remission still had RUNX1 mutation. The patients with RUNX1 mutations were older than those with wild-type RUNX1. (p=0.006) and RUNX1 mutation had a trend of male preponderance. The WBC count and blast percentage of peripheral blood and bone marrow were not different according to RUNX1 mutational status. The complete response rate was significantly lower in RUNX1 mutated group compared with wild-type group. (57% vs. 84%, p=0.005) In univariable survival analysis, RUNX1 mutations were significantly associated with inferior event-free survival (EFS) (p<0.001), relapse-free survival (RFS) (p=0.009) and overall survival (OS) (p=0.002). However, in multivariable analysis, RUNX1 mutation was not an independent prognostic factor for inferior EFS (hazard ratio(HR) 1.48, p=0.286), RFS (HR 2.15, p=0.057) OS (HR 1.14, p=0.716). Co-mutation analysis revealed that ASXL1 (26%,p=0.001), KRAS (26%, p=0.009), BCOR (16%, p=0.032) were correlated with RUNX1 mutation. None of the patients with RUNX1 mutation had NPM1 mutation and only one patient had CEBPA mutation. Conclusion In cytogenetically normal AML, RUNX1 mutation is observed in 5.4% and is mutually exclusive of the NPM1 and CEBPA mutation. Older age and lower complete response rate is correlated with RUNX1 mutation. In univariable survival analysis, RUNX1 mutation is associated with poor clinical outcomes. Disclosures No relevant conflicts of interest to declare.

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More sources

Dissertations / Theses on the topic "Mutation"

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Komp, Lindgren Patricia. "Mutations and Mutation Rate in the Development of Fluoroquinolone Resistance." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8275.

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Ibrahim, Daniel Murad. "ChIP-seq reveals mutation-specific pathomechanisms of HOXD13 missense mutations." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2015. http://dx.doi.org/10.18452/17102.

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Mutationen von Transkriptionsfaktoren (TF) betreffen nicht nur die Funktion des TFs, sondern auch die Expression seiner Zielgene und liegen häufig angeborenen Entwicklungsdefekten zugrunde. Über 20 Mutationen in HOXD13, einem TF der die Entwicklung der Extremitäten kontrolliert, sind bisher als Ursache verschiedenartiger Extremitätenfehlbildungen entdeckt worden. Eine molekularbiologische Grundlage für die Vielgestaltigkeit der HOXD13-Mutationen ist jedoch unbekannt. Die bisherigen Methoden zur funktionellen Charakterisierung von TF-Mutationen ermöglichten eine lediglich eingeschränkte Interpretation der molekularen Pathomechanismen. Die kürzlich entwickelte ChIP-seq Methode ermöglicht eine umfassende, funktionelle Charakterisierung eines TFs. In dieser Arbeit wurde eine Methode etabliert, um eine Vielzahl von Transkriptionsfaktoren und TF-Mutationen systematisch zu untersuchen. Zur Validierung wurden zwei neue Punktmutationen in HOXD13, p.Q317K und p.R298Q, charakterisiert. Beide Mutationen betreffen die DNA-bindende Domäne von HOXD13, rufen aber stark unterschiedliche Fehlbildungen hervor. Die Ergebnisse zeigen, dass die HOXD13Q317K Mutante eine veränderte Sequenzspezifität aufweist, welche nun jener eines anderen TFs, PITX1, ähnelt. Auch genomweit zeigt HOXD13Q317K ein Bindungsprofil, welches eher PITX1 als HOXD13wt entspricht. Durch weitere, unabhängige Analysen und Experimente wurde bestätigt, dass die p.Q317K Mutation HOXD13 in einen TF mit PITX1-ähnlichen Eigenschaften verändert. Die HOXD13R298Q-Mutante zeigt eine weitgehend unveränderte Bindungssequenz gegenüber HOXD13wt, jedoch eine veränderte Zusammensetzung der genomischen Bindestellen. Dies weist, in Kombination mit dem humanen Phänotyp auf einen dominant-negativen Pathomechanismus dieser Mutanten hin. Zusammengenommen zeigt diese Arbeit durch die Erhebung von experimentellen Daten, dass klar unterscheidbare molekularbiologische Mechanismen den HOXD13Q317K- und HOXD13R298Q-Mutationen zugrunde liegen.
Mutations in transcription factors (TF) do not only affect the function of the TF, but also the expression of its target genes and are frequently underlying congenital malformations. More than 20 distinct pathogenic mutations in HOXD13, a TF controlling limb development, have been associated with a broad range of limb malformations. However, a molecular basis underlying the variability of HOXD13-associated phenotypes remains elusive. To date, the experimental methods used to functionally characters TF mutations have allowed only limited insights into the underlying molecular pathomechanisms. The recently developed ChIP-seq technology has proven to be a powerful method to profile the binding characteristics of TFs; however a number of technical hurdles hinder its application for functional characterization of mutant TFs. This work describes the establishment of a ChIP-seq approach to investigate a wide spectrum of TFs and TF mutations. The approach was applied to characterize two previously unknown missense mutations in HOXD13, p.Q317K and p.R298Q, which both alter the DNA-binding domain of HOXD13 but cause very different disease phenotypes. The results show that the HOXD13Q317K mutant has an altered sequence specificity that resembles the recognition sequence of another TF, PITX1. Further, the genome-wide binding pattern of HOXD13Q317K shifts towards a more PITX1-like binding pattern. Even further analysis and viral overexpression in chicken limb buds confirm that the mutation partially converts HOXD13Q317K into a TF with PITX1-like properties. The HOXD13R298Q has a largely unchanged sequence specificity, but an altered composition of genomic binding sites. This, in combination with the human phenotype, indicates that the mutant might act in a dominant-negative manner. Collectively, this work shows through generation of direct experimental evidence, that clearly distinct molecular mechanisms underlie the pathogenicity of HOXD13Q317K and HOXD13R298Q mutations.

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Hagman, Hans. "Mutation Testing : A comparison of mutation selection methods." Thesis, Högskolan i Skövde, Institutionen för kommunikation och information, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-6569.

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Software is all around us in our lives in the industrialized world, and we as a society and individuals need it to function correctly. Software testing fills the role of performing behavior audits, to guide the correction of the software to its intended behavior. The consequences of faulty software can range to the late arrival of trains, to nuclear meltdowns. This places quality requirements on the software of various levels. Program based mutation testing provides a high level of faultfinding capability. It does this by injecting many synthetic faults into the code under test, as described by mutation operators. These faults are used to search for testcases that would identify such faults, and consequently find real faults that the synthetic faults mimic. However, mutation testing is costly on three accounts; each mutant of the original code is compiled, each mutant should ideally have an associated testcase to reveal that fault the mutant contains, finally the testcases are analyzed thoroughly by looking the output of the original and mutants to reveal the error in behavior. In order to reduce cost while maintaining a high level of faultfinding, selective mutation testing is investigated, it uses a subset of all the available mutation operators. The investigation found that using Absolute value-, and Relational operator-, mutation reduces cost of mutation testing by 80%, while uncovering 83% of the injected faults.

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Krasovec, Marc. "Estimation des taux de mutation : implications pour la diversification et l'évolution du phytoplancton eucaryote." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066371/document.

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Les mutations sont la principale source de diversité sur laquelle agit la sélection pour permettre aux espèces de s'adapter. Les études de l'effet des mutations sur la survie et du taux de mutation sont donc essentielles pour mieux comprendre l'évolution. Par une approche d'expérience d'accumulation de mutations, nous étudions ces deux questions chez cinq modèles d'algues vertes (Ostreococcus tauri, O. mediterraneus, Bathycoccus prasinos, Micromonas pusilla, et Picochlorum RCC4223). Il est mis en évidence une diminution de la fitness au cours du temps en raison des mutations délétères, et une importante interaction génotype-environnement sur l'effet des mutations. Le taux de mutation varie aux échelles intra-génomique et inter-spécifique, avec deux principaux résultats: une augmentation du taux de mutation dans les régions non codantes et une augmentation du taux de mutation avec la taille du génome chez les eucaryotes et en fonction de l'écart à l'équilibre en GC du génome. Aussi, l'assemblage et l'annotation d'une picoalgue du genre Picochlorum permettent d'étudier le rôle des transferts horizontaux de gènes chez les Chlorophytes
Mutations are the main source of diversity on which selection acts to allow species to adapt. Studies of the effect of mutations on survival and estimation of spontaneous mutation rates are essential to better understand evolution. Using mutation accumulation experimental approach, we investigated the issues of mutation effects and mutation rate in five models of green algae (Ostreococcus tauri, O. mediterraneus, Bathycoccus Prasinos, Micromonas pusilla, and Picochlorum RCC4223). It highlighted a decline in fitness over time because of deleterious mutations, and a significant genotype-environment interaction on the fitness effect of mutations. The mutation rate varies at inter-specific and intra-genomic scales, with two main results: a raise of the mutation rate in non-coding regions in accordance with trancriptional-coupled repair, and an increase of the mutation rate with an increase of the genome size in eukaryotes and the GC content deviation from the equilibrium. Also, a new Picochlorum genome is provided to investigate the role of horizontal gene transfer in the Chlorophyta group

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Krasovec, Marc. "Estimation des taux de mutation : implications pour la diversification et l'évolution du phytoplancton eucaryote." Electronic Thesis or Diss., Paris 6, 2016. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2016PA066371.pdf.

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Les mutations sont la principale source de diversité sur laquelle agit la sélection pour permettre aux espèces de s'adapter. Les études de l'effet des mutations sur la survie et du taux de mutation sont donc essentielles pour mieux comprendre l'évolution. Par une approche d'expérience d'accumulation de mutations, nous étudions ces deux questions chez cinq modèles d'algues vertes (Ostreococcus tauri, O. mediterraneus, Bathycoccus prasinos, Micromonas pusilla, et Picochlorum RCC4223). Il est mis en évidence une diminution de la fitness au cours du temps en raison des mutations délétères, et une importante interaction génotype-environnement sur l'effet des mutations. Le taux de mutation varie aux échelles intra-génomique et inter-spécifique, avec deux principaux résultats: une augmentation du taux de mutation dans les régions non codantes et une augmentation du taux de mutation avec la taille du génome chez les eucaryotes et en fonction de l'écart à l'équilibre en GC du génome. Aussi, l'assemblage et l'annotation d'une picoalgue du genre Picochlorum permettent d'étudier le rôle des transferts horizontaux de gènes chez les Chlorophytes
Mutations are the main source of diversity on which selection acts to allow species to adapt. Studies of the effect of mutations on survival and estimation of spontaneous mutation rates are essential to better understand evolution. Using mutation accumulation experimental approach, we investigated the issues of mutation effects and mutation rate in five models of green algae (Ostreococcus tauri, O. mediterraneus, Bathycoccus Prasinos, Micromonas pusilla, and Picochlorum RCC4223). It highlighted a decline in fitness over time because of deleterious mutations, and a significant genotype-environment interaction on the fitness effect of mutations. The mutation rate varies at inter-specific and intra-genomic scales, with two main results: a raise of the mutation rate in non-coding regions in accordance with trancriptional-coupled repair, and an increase of the mutation rate with an increase of the genome size in eukaryotes and the GC content deviation from the equilibrium. Also, a new Picochlorum genome is provided to investigate the role of horizontal gene transfer in the Chlorophyta group

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6

Lee, Angela Waishan. "Hair-loss mutation (dep) caused by a mutation in palmitoyl transferase Zdhhc21." Thesis, University of Edinburgh, 2008. http://hdl.handle.net/1842/29217.

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The recessive hair loss mutant, dep, contains a mutation (del-233F) at the C-terminal of Zdhhc21. Wild-type Zdhhc21 has been shown to enhance palmitoylation of several specific substrates in a transfected cell assay. Zdhhc21 localises to the cis-Golgi, whereas the mutant protein is mislocalised and is inactive in palmitoylation. We verified the candidacy of Zdhhc21 by transgenic BAC rescue. Dep is characterised by progressive hair loss, hyperplasia of the sebaceous glands, the interfollicular epidermis and the outer root sheath. In-situ hybridisation and immunohistochemistry show that both wild-type and dep mRNA and protein are present in the inner root sheath (IRS). Phenotypic characterisation using molecular markers in cell culture and on skin sections reveals abnormalities that suggest a lack of correct hair shaft differentiation in dep. We speculate that dep may have a direct or indirect effect on 4 members of the Wnt family – essential regulators of hair shaft differentiation – because of their co-expression in the IRS and because the dep mutant exhibits a Wnt-deficient phenotype. This hypothesis may provide an example of how local signalling centres may be established to allow for spatiotemporal gene expression. Furthermore, dep is the first mouse model that provides direct evidence of an enzymatic activity of the Dhhc family.

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Drechsel, Dieter. "Evolution and Mutation Physics." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-69962.

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Base rivalry arises at replication of monotonous DNA – sequences. Irreparable mutations can arise by tunnel processes if the developed energy is high enough. The tunnel probability depends not only on the base rivalry energy but also depends on the temperature of surroundings. The tunnel probability diminishes with decreasing temperature. The cytoplasm viscosity increases in the long term with decreasing temperature. The length of the monotonous sequence in which happens an irreparable mutation (caused by base rivalry) then will be larger than at higher temperatures. This means that the possible distribution variety of all base components on the given matrix will diminish; therefore the probability increases that one base component which possesses the necessary energy, comes into the certain monotonous sequence to provoke a tunnel process. These different temperature dependences are the subject of the following examinations; they lead to the equation (32) which is valid for coming off of an irreparable mutation which is caused by base rivalry. Because of the dependence between temperature change and mutating sequence length from s1 to s1+1 (expressed in this equation), there result informations about evolution, and informations about mutation of DNA – viruses. The calculations are performed with very small DNA fragments so called residual fragments.

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Duncan, Ishbel M. M. "Strong mutation testing strategies." Thesis, Durham University, 1993. http://etheses.dur.ac.uk/5771/.

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Mutation Testing (or Mutation Analysis) is a source code testing technique which analyses code by altering code components. The output from the altered code is compared with output from the original code. If they are identical then Mutation Testing has been successful in discerning a weakness in either the test code or the test data. A mutation test therefore helps the tester to develop a program devoid of simple faults with a well developed test data set. The confidence in both program and data set is then increased. Mutation Analysis is resource intensive. It requires program copies, with one altered component, to be created and executed. Consequently, it has been used mainly by academics analysing small programs. This thesis describes an experiment to apply Mutation Analysis to larger, multi-function test programs. Mutations, alterations to the code, are induced using a sequence derived from the code control flow graph. The detection rate of live mutants, programs whose output match the original, was plotted and compared against data generated from the standard technique of mutating in statement order. This experiment was repeated for different code components such as relational operators, conditional statement or pointer references. A test was considered efficient if the majority of live mutants was detected early in the test sequence. The investigations demonstrated that control flow driven mutation could improve the efficiency of a test. However, the experiments also indicated that concentrations of live mutants of a few functions or statements could effect the efficiency of a test. This conclusion lead to the proposal that mutation testing should be directed towards functions or statements containing groupings of the code component that give rise to the live mutants. This effectively forms a test focused onto particular functions or statements.

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Williamson, David. "Haemoglobin mutation and instability." Thesis, Open University, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.315297.

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Jia, Y. "Higher order mutation testing." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1401264/.

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Mutation testing is a fault-based software testing technique that has been studied widely for over three decades. To date, work in this field has focused largely on first order mutants because it is believed that higher order mutation testing is too computationally expensive to be practical. This thesis argues that some higher order mutants are potentially better able to simulate real world faults and to reveal insights into programming bugs than the restricted class of first order mutants. This thesis proposes a higher order mutation testing paradigm which combines valuable higher order mutants and non-trivial first order mutants together for mutation testing. To overcome the exponential increase in the number of higher order mutants a search process that seeks fit mutants (both first and higher order) from the space of all possible mutants is proposed. A fault-based higher order mutant classification scheme is introduced. Based on different types of fault interactions, this approach classifies higher order mutants into four categories: expected, worsening, fault masking and fault shifting. A search-based approach is then proposed for locating subsuming and strongly subsuming higher order mutants. These mutants are a subset of fault mask and fault shift classes of higher order mutants that are more difficult to kill than their constituent first order mutants. Finally, a hybrid test data generation approach is introduced, which combines the dynamic symbolic execution and search based software testing approaches to generate strongly adequate test data to kill first and higher order mutants.

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Books on the topic "Mutation"

1

Robin, Cook. Mutation. New York: Putnam's, 1989.

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Applegate, Katherine. Mutation. London: Scholastic, 2002.

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Robin, Cook. Mutation. London: Guild Publishing, 1989.

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Robin, Cook. Mutation. London: Pan Books, 1989.

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Robin, Cook. Mutation. New York: Berkley Books, 1990.

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Robin, Cook. Mutation. New York: Putnam, 1989.

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1962-, Cordy Michael, ed. Mutation: Roman. München: Diana-Verl., 2000.

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Logie, Colin. Point mutation. Rijeka: InTech, 2012.

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Applegate, Katherine. The mutation. Milwaukee, WI: Gareth Stevens Pub., 2000.

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Applegate, Katherine. The mutation. London: Hippo, 2001.

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Book chapters on the topic "Mutation"

1

Konzak, C. F. "Mutations and Mutation Breeding." In Agronomy Monographs, 428–43. Madison, WI, USA: American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, 2015. http://dx.doi.org/10.2134/agronmonogr13.2ed.c24.

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Lee, L. Slade, Bradley J. Till, Helen Hill, Owen A. Huynh, and Joanna Jankowicz-Cieslak. "Mutation and Mutation Screening." In Methods in Molecular Biology, 77–95. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-715-0_8.

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Smith, C. A., and E. J. Wood. "Mutation." In Molecular Biology and Biotechnology, 156–84. Boston, MA: Springer US, 1991. http://dx.doi.org/10.1007/978-1-4615-3866-0_8.

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Vogel, Friedrich, and Arno G. Motulsky. "Mutation." In Human Genetics, 334–432. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-662-02489-8_6.

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Brennan, Michael. "Mutation." In Encyclopedia of Personality and Individual Differences, 3057–58. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-24612-3_1551.

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Doolittle, Donald P. "Mutation." In Advanced Series in Agricultural Sciences, 74–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71734-5_15.

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Shekhar, Shashi, and Hui Xiong. "Mutation." In Encyclopedia of GIS, 765. Boston, MA: Springer US, 2008. http://dx.doi.org/10.1007/978-0-387-35973-1_857.

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Smith-Keary, Peter. "Mutation." In Molecular Genetics, 182–203. London: Macmillan Education UK, 1991. http://dx.doi.org/10.1007/978-1-349-11732-1_11.

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Lázaro, Ester. "Mutation." In Encyclopedia of Astrobiology, 1102–3. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_1037.

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Forsdyke, Donald R. "Mutation." In Evolutionary Bioinformatics, 131–51. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-7771-7_7.

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Conference papers on the topic "Mutation"

1

Souza, Beatriz, and Rohit Gheyi. "A Lightweight Technique to Identify Equivalent Mutants." In XI Congresso Brasileiro de Software: Teoria e Prática. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/cbsoft_estendido.2020.14630.

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Mutation analysis is a popular but costly approach to assess the quality of test suites. Equivalent mutants are useless and contribute to increase costs. We propose a lightweight technique to identify equivalent mutants by proving equivalences with Z3 in the context of weak mutation testing. To evaluate our approach, we apply our technique for 40 mutation targets (mutations of an expression or statement) and automatically identify 13 equivalent mutations for seven mutation targets. We manually confirm that the equivalent mutants detected by our technique are indeed equivalent. Moreover, we evaluate our approach in the context of strong mutation testing against mutants generated by MuJava for 5 projects. Our technique detects all equivalent mutants detected by TCE. The results of our technique can be useful to improve mutation testing tools by avoiding the application of 13 mutations for 7 mutation targets.

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Cambraia, Amanda, Mario Campos Junior, Fernanda Gubert, Juliana Ferreira Vasques, Marli Pernes da Silva Loureiro, Claudio Heitor Gress, José Mauro Bráz de Lima, Rosalia Mendez Otero, and Verônica Marques Zembrzuski. "A novel mutation in the RRM2 domain of TDP-43 in a Brazilian sporadic ALS patient." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.486.

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Introduction: Amyotrophic Lateral Sclerosis (ALS) is an adult-onset progressive and fatal neurodegenerative disease that selectively affects upper and lower motor neurons. Death occurs within 3 to 5 years of onset, usually from respiratory complications. Most cases of ALS are sporadic (SALS), but familial forms of the disease (FALS) represent approximately 10% of the cases. More than 30 genes have been associated with ALS and mutations in these genes account for more than a half of all familial cases and about 10% of sporadic cases. One of the most prevalent genes is TARDBP, responsible for approximately 4-6% of FALS and nearly 1-2% of SALS cases. The aim of this study was to perform the screening of known ALS genes, to increase the knowledge of the mutations that circulate in the population from Rio de Janeiro. Methods: The screening of mutations was performed through the Illumina Next Generation Sequencing (NGS) platform with the use of a sequencing panel that contained the TARDBP, SOD1, FUS, VAPB, SMN1 and SMN2 genes. Results: A novel missense mutation (p.Phe194Leu) in exon 5 of the TARDBP gene was found in a sporadic male patient who died at the age of 58 (2018). The mutation, a TTT/CTT substitution, was not detected in any mutation databases and in the literature. In silico analysis of this variant with different algorithms were performed and the results pointed to a probably damaging impact and that the mutation is disease causing. Conclusion: Through the study of the ALS genes by the NGS, we were able to identify a novel TARDBP mutation in a non-familial ALS patient. In addition, this study also increases the number of known TARDBP mutations in ALS patients and our knowledge of the mutations that affect the patients from of population from Rio de Janeiro.

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Offutt, Jeff, Paul Ammann, and Lisa (Ling) Liu. "Mutation Testing implements Grammar-Based Testing." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.11.

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Sen, Sagar, and Benoit Baudry. "Mutation-based Model Synthesis in Model Driven Engineering." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.12.

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Gallardo, Guillermo, John May, and Julio C. Gallardo. "Assessment of Data Diversity Methods for Software Fault Tolerance Based on Mutation Analysis." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.1.

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Bradbury, Jeremy S., James R. Cordy, and Juergen Dingel. "Mutation Operators for Concurrent Java (J2SE 5.0)." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.10.

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Tuya, Javier, Ma Jose Suarez-Cabal, and Claudio de la Riva. "SQLMutation: A tool to generate mutants of SQL database queries." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.13.

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Crouzet, Yves, Helene Waeselynck, Benjamin Lussier, and David Powell. "The SESAME Experience: from Assembly Languages to Declarative Models." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.14.

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Belli, Fevzi, Christof J. Budnik, and W. Eric Wong. "Basic Operations for Generating Behavioral Mutants." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.2.

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Anbalagan, Prasanth, and Tao Xie. "Efficient Mutant Generation for Mutation Testing of Pointcuts in Aspect-Oriented Programs." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.3.

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Reports on the topic "Mutation"

1

Silverstein, Eva. Dimensional Mutation and Spacelike Singularities. Office of Scientific and Technical Information (OSTI), October 2005. http://dx.doi.org/10.2172/878029.

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Neel, J. V. Studies of human mutation rates. Office of Scientific and Technical Information (OSTI), July 1991. http://dx.doi.org/10.2172/5025881.

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Neel, J. V. Studies of human mutation rates. Office of Scientific and Technical Information (OSTI), January 1990. http://dx.doi.org/10.2172/6368357.

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Neel, J. V. The study of human mutation rates. Office of Scientific and Technical Information (OSTI), January 1992. http://dx.doi.org/10.2172/7175958.

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Harris, Reuben S. Enzyme-Catalyzed Mutation in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, August 2014. http://dx.doi.org/10.21236/ada613711.

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Andrews, Paul W., Raymond R. Tice, and Diane Satterfield. Salmonella Typhimurium Microsome Reverse Mutation Assay. Fort Belvoir, VA: Defense Technical Information Center, March 1996. http://dx.doi.org/10.21236/ada589278.

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Ponder, Rebecca, and Susan Rosenberg. Mechanism of Mutation in Non-Dividing Cells. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada396622.

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Petrosino, Joseph F. Mechanisms of Mutation in Non-Dividing Cells. Fort Belvoir, VA: Defense Technical Information Center, May 2002. http://dx.doi.org/10.21236/ada406067.

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Ponder, Rebecca G., and Susan Rosenberg. Mechanism of Mutation in Non-Dividing Cells. Fort Belvoir, VA: Defense Technical Information Center, July 2002. http://dx.doi.org/10.21236/ada408728.

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Petrosino, Joseph F., and Susan Rosenberg. Mechanisms of Mutation in Non-Dividing Cells. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada416708.

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