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Search Results: 1 - 10 of 1846 matches for " mutation "
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A New Method for Fastening the Convergence of Immune Algorithms Using an Adaptive Mutation Approach  [PDF]
Mohammed Abo-Zahhad, Sabah M. Ahmed, Nabil Sabor, Ahmad F. Al-Ajlouni
Journal of Signal and Information Processing (JSIP) , 2012, DOI: 10.4236/jsip.2012.31011
Abstract: This paper presents a new adaptive mutation approach for fastening the convergence of immune algorithms (IAs). This method is adopted to realize the twin goals of maintaining diversity in the population and sustaining the convergence capacity of the IA. In this method, the mutation rate (pm) is adaptively varied depending on the fitness values of the solutions. Solutions of high fitness are protected, while solutions with sub-average fitness are totally disrupted. A solution to the problem of deciding the optimal value of pm is obtained. Experiments are carried out to compare the proposed approach to traditional one on a set of optimization problems. These are namely: 1) an exponential multi-variable function; 2) a rapidly varying multimodal function and 3) design of a second order 2-D narrow band recursive LPF. Simulation results show that the proposed method efficiently improves IA’s performance and prevents it from getting stuck at a local optimum.
Genetic risk factors and retinal ganglion cell degeneration in primary open-angle glaucoma (POAG): A bird’s eye view  [PDF]
Barkur S. Shastry
Advances in Bioscience and Biotechnology (ABB) , 2013, DOI: 10.4236/abb.2013.45082
Abstract: Glaucoma is an optic neuropathy and often associated with elevated intraocular pressure (IOP). It is the second leading cause of irreversible blindness worldwide and is characterized by the optic nerve degeneration and loss of retinal ganglion cells (RGCs). This may lead to loss of vision. The primary cause of glaucoma is unknown but several risk factors including elevated IOP and age have been suggested. In most population, primary open-angle glaucoma (POAG) is the most common type of glaucoma and is often associated with elevated IOP. Genetic analyses have identified at least 14 chromosomal loci but only three genes which when mutated can cause POAG have been well documented. These genes account for less than 5% of all POAG cases suggesting that more than 90% of the genetic contribution of POAG cases is unknown. RGC consists of cell body, axon and dendritic arbor and each of these three parts can independently degenerate. Several molecular signals such as oxidative stress, mitochondrial dysfunction, disruption of neurotrophic factor (NTF), dysfunction of immune system, glial activation and the release of tumor necrosis factor (TNF) have been found to be involved in the optic nerve degeneration. Therefore, therapies aimed at axonal and cell body protection may have a greater protective role in early or progressive glaucoma. In the future, an understanding of gene-gene and gene-environmental factor interaction as well as epigenetic regulation of gene expression by environmental factors may provide an opportunity to develop neuroprotective therapies and DNA based diagnostic tests.
Towards Semantic Mutation Testing of Aspect-Oriented Programs  [PDF]
Abdul Azim Abdul Ghani
Journal of Software Engineering and Applications (JSEA) , 2013, DOI: 10.4236/jsea.2013.610A002

Aspect-oriented programs have received much attention from software testing researchers. Various testing techniques and approaches have been proposed to tackle issues and challenges when testing aspect-oriented programs including traditional mutation testing. In traditional mutation testing of aspect-oriented programs, mutants are generated by making small changes to the syntax of the aspect-oriented language. Recently, a new approach known as semantic mutation testing has been proposed. This approach mutates the semantics of the language in which the program is written. The mutants generated misunderstandings of the language which are different classes of faults. Aspect-oriented programming presents itself with different properties that can be further explored with respect to semantic mutation testing. This paper describes various possible scenarios that semantic mutation testing strategy might have particular value in testing aspect-oriented programs.

Antiretroviral-Drug Resistant Mutations and Genetic Diversity in HIV-1 Infected Individuals in Nigeria  [PDF]
Olubunmi Ruth Negedu-Momoh, Olayeni Stephen Olonitola, Lillian Emiola Odama, Helen Ineigo Inabo, Henry Akwen Mbah, Alex Nganga Kasembeli, Seth Chekata Inzaule, Edward Adekola Oladele, Titilope Badru, Simon Magaji Agwale
World Journal of AIDS (WJA) , 2014, DOI: 10.4236/wja.2014.42024

Introduction: Despite the success derived from antiretroviral therapy, drug resistance (DR) mutations are known to develop and are major impediments to treatment of HIV patients. Therefore, periodic assessment of HIVDR is needed to ensure continuous HAART efficacy. This study assessed the magnitude of drug resistance as well as HIV genetic variability in drug-naive and treated patients in Nigeria. Methodology: Genotypic analysis was performed by sequencing plasma specimens from 40 individuals in a cross sectional study involving 202 HIV infected patients from all the six geopolitical zones of Nigeria. Sequences were analyzed for presence of HIVDR mutation using the algorithm in Stanford HIVDR database and confirmed by IAS-USA 2009 mutation list. Phylogenetic and recombination analyses were done using PAUP V4.0 and REGA V2.0 respectively. Results: Major DR mutations were detected in the reverse transcriptase (RT) gene of 5 (33%) drug experienced and 2 (8%) na?ve patients. Most common mutations were M184V and K103N with no protease (PR) mutations detected. Thymidine analogue mutations (TAMs) and a complex multi resistance mutation Q151M were detected in 3 samples. Polymorphic substitutions were observed in both PR and RT gene. Phylogenetic analysis revealed Group M isolates of G (20), J (1), circulating recombinant forms: CRF02_AG (14), CRF-18-cpx (1), CRF06_cpx (3) and a unique AD recombinant (1). Conclusion: Our findings corroborate previous studies on circulating DR viruses in Nigeria while genetic diversity is on the increase. In view of ART scale-up, monitoring the resistance pattern and genetic diversity will aid in appropriate prevention strategies.

Testing the Mutation Accumulation Theory of Aging Using Bioinformatic Tools  [PDF]
Abdullah Salah Elamoudi
Advances in Aging Research (AAR) , 2018, DOI: 10.4236/aar.2018.72002
Abstract: Objective: An interplay of many variant mechanisms is thought to underlie aging or senescence. The Mutation Accumulation Theory proposes the accumulation of mutations in proteins to engender their aging phenotype. Testing whether random mutations lead to the aging phenotype was never done and is deemed infeasible. Bioinformatic algorithms provide an a-priori approach that allows testing; they employ prior knowledge of well-studied proteins to predict the changes brought on by mutations. Here, the Mutation Accumulation Theory of aging is tested using such bioinformatic tools. Methods: This is a simulation study, conducted 2017, September, using algorithms with Web accessibility. Three well-studied proteins implicated in aging were chosen: Collagen, Beta-amyloid Precursor Protein (β-APP) and Low-density-lipoprotein-receptor (LDL-receptor). Random mutations were introduced to their native coding sequences. Then, the mutated sequences were tested using three different prediction algorithms: SPpred for solubility, I-mutant for stability (delta-free energy), SNP and GO for pathogenicity. The new mutated phenotype was then correlated to the aging phenotype of the protein; decrease in solubility for Collagen and β-APP; and accelerated atherosclerosis for LDL-receptor. Results: 15 mutated variants for each protein (45 in total). For collagen and β-APP, the SPpred algorithm did not predict changes in solubility of the naked protein, but the I-mutant and SNP and GO definitely predicted changes that fit the aging phenotype. However, for LDL-receptors, none of the mutated variants when studied could account for the aging phenotype. Conclusion: for Collagen and β-APP, it is shown here that random mutations and their accumulation could explain the aging phenotype of both proteins; backing the Mutation Accumulation Theory for aging.
Ongoing Mutations in Polytreated Metastatic Cancer Patients May Create a New Chance of Treatment with Unexpected Drugs  [PDF]
Mahmoud M. Abbass Ellithy, Amr Shafik Saad, Mahmoud Salah Abdelsalam, Amr Elsebaei
Journal of Cancer Therapy (JCT) , 2018, DOI: 10.4236/jct.2018.911069
Abstract: Objectives: In this study molecular/genomic characteristics were done on new tissue biopsies taken from Egyptian patients with refractory metastatic solid tumors aiming for two end points: To figure out a personalized treatment and to find the percent of discrepancy between the elaborated drugs of potential benefit and that stated in the guidelines. Methods: 22 eligible patients joined the study. (breast = 5, colon = 3, liver = 2, kidney = 2, ovary = 2, sarcoma = 2, metastasis of unknown origin = 2, Tongue = 1, Adrenal cancer = 1, gastric = 1 and lung cancer = 1). Biopsies were subjected to one or more of the following tests; Immunohistochemistry, Chromogenic/Fluorescence in situ Hybridization, Next Generation Sequencing, Sanger Sequencing. Results: Biomarkers and their corresponding drugs with associated potential benefits were detected as following; TUBB3, PGP and TLE3 (indicating potentiality of paclitaxel) in 22% of cases, TS (Antifolates) 18%, TOPO1 (Irinotecan) 14%, RRM1 (Gemcitabine) 13%, MGMT (Temozolomide) 7%, TOPO2 (Doxorubcin) 7%, ERCC1 (Platinum) 6%, BRAF (Vemurafenib) 2%, KRAS and NRAS (anti EGFR) 2%, C-KIT (TKIs potentiality) 1%, hormonal receptors in 5% of cases (Antihormonal potentiality), monoSPARK and polySPARK in 3% of cases indicating nabpaclitaxel potentiality. Potentiality of some drugs (Based on their corresponding biomarkers) was unexpectedly detected as following; Pemetrexed, irinotecan, dacarbazine and temozolomide in breast cancer patients, platinums and taxanes in liver, Taxanes, gemcitabine, fluoropyramidines, pemetrexed, dacarbazine and temozolomide in kidney cancer, Taxanes, gemcitabine, pemetrexed, dacarbazine and temozolomide in cancer colon, irinotecan in cancer tongue, Pemetrexed and irinotecan in adrenal gland cancer. The percentage of drugs of potential benefit that is not stated in the guidelines case by case was as following: Breast (12%, 15%, 23%, 31%, 21%), Colon (38.1%, 26.5%, 27%), Liver (33.5%, 25%), Kidney (15%, 29%), Ovary (1%, 2%) Sarcoma (17%, 53.5%) tongue 35%, adrenal 73.2%, Gastric 27.8% and lung 36%. Conclusion: Studying molecular/genomic
Breeding Sorghum Using Induced Mutations: Future Prospect for Namibia  [PDF]
Maliata Athon Wanga, A. Ashok Kumar, Grace Nandesora Kangueehi, Hussein Shimelis, Lydia N. Horn, Fatma Sarsu, Jahanna F. N. Andowa
American Journal of Plant Sciences (AJPS) , 2018, DOI: 10.4236/ajps.2018.913196
Abstract: In arid and semi-arid regions of the world sorghum stands out as a climate change-ready crop with high potential for the production of food, feed, fodder, fiber and fuel in the face of increasing human population. The present review highlights induced mutation breeding technique as a potential tool for improving sorghum in Namibia. The review discussed the following issues; crop improvement using mutagens, mutant screening, selection and evaluation, impact of induced mutation breeding, factors for declining production and future implication of sorghum mutation breeding. In Namibia, severe drought stress resulting in total crop failure has become frequent. This is partly a consequence of farmers growing crop varieties which cannot withstand impact of drought. As such Namibia has limited drought tolerant varieties available for the diverse agro-ecologies. Farmers keep growing the familiar landraces which performs well in good rainfall years but fails to produce stable yield with irregular and erratic rainfall. Thus, breeding new sorghum varieties of high yield and quality combined with multiple agronomic traits including pest and disease resistance and high efficiency in nutrient and water use is needed. Induced mutation is one of the breeding methods utilized worldwide to supplement conventional breeding for developing superior varieties with desirable traits in different crops. Development of high yielding, drought tolerant, and dwarf sorghums with early maturity enables effective utilization of available soils moisture and in optimizing plant density for achieving higher yield in farmers’ fields. Recombination breeding through exploitation of natural genetic variability and mutation breeding to reduce the plant height without disturbing agronomic superiority of elite lines is recommended for sorghum improvement in Namibia.
Inferring Deleterious-Mutation Parameters in Natural Daphnia Populations
Deng Hong-Wen
Biological Procedures Online , 1998, DOI: 10.1251/bpo3
Abstract: Deng and Lynch (1, 2) proposed to characterize deleterious genomic mutations from changes in the mean and genetic variance of fitness traits upon selfing in outcrossing populations. Such observations can be readily acquired in cyclical parthenogens. Selfing and life-table experiments were performed for two such Daphnia populations. A significant inbreeding depression and an increase of genetic variance for all traits analyzed were observed. Deng and Lynch's (2) procedures were employed to estimate the genomic mutation rate (U), mean dominance coefficient ( ), mean selection coefficient ( ), and scaled genomic mutational variance ( ). On average, , , and (^ indicates an estimate) are 0.84, 0.30, 0.14 and 4.6E-4 respectively. For the true values, the and are lower bounds, and and upper bounds.
Filaggrin mutations are associated with ichthyosis vulgaris in the Southern Chinese population  [PDF]
Chang-Xing Li, Quan Luo, Xue-Mei Li, Xi-Bao Zhang, Chun-Lei Han, Ze-Lin Ma, Dong-Zi Lin
Health (Health) , 2010, DOI: 10.4236/health.2010.212200
Abstract: Filaggrin (FLG) plays an important role in the epidermal barrier function, which identified in patients with ichthyosis vulgaris(IV).To study the genetics of FLG mutations in Southern Chinese patients with IV. We evaluated the influence of five mutations (3321 delA, 441delA, 1249 insG, E1795X and S3296X) in a cohort of 65 IV Chinese patients and in 100 control individuals using the Sequenom® MassARRAY® system. The null allele frequency of 3321delA was 52.31%(34/65). FLG mutation 441delA was only found in one IV patients. FLG mutations 1249insG, E1795X and S3296X were not found in these patients. These findings show that the mutation 3321delA represent the most frequent genetic cause in Southern Chinese IV patients. Our findings confirm and extend the knowledge of the influence of FLG mutations in IV.
Prediction of mutation position, mutated amino acid and timing in hemagglutinins from North America H1 influenza A virus  [PDF]
Shao-Min Yan, Guang Wu
Journal of Biomedical Science and Engineering (JBiSE) , 2009, DOI: 10.4236/jbise.2009.22021
Abstract: This study was trying to predict the mutations in H1 hemagglutinins of influenza A virus from North America including the predictions of mu-tation position, the predictions of would-be-mutated amino acids and the predictions of time of occurrence of mutations. The results paved a possible way for accurate, precise and reliable prediction of mutation in proteins from influenza A virus.
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