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Environmental Disease
Published in Gary S. Moore, Kathleen A. Bell, Living with the Earth, 2018
Gary S. Moore, Kathleen A. Bell
Many human diseases are associated with genetic defects. These defects can occur as (1) single-gene defects known as a point mutations or base substitutions or (2) cytogenetic defects in which there are abnormalities in the number or structure of chromosomes. A point mutation occurs when a single nucleotide base is replaced at one point in the DNA molecule with a different base. The DNA replicates with a substituted base pair such that A:T might be substituted for C:G. This base substitution could result in the incorporation of an incorrect amino acid into a synthesized protein, thereby rendering the protein less active or inactive. The resulting effect may be imperceptible or neutral or may result in one of many serious human ailments such as cystic fibrosis (CF), phenylketonuria (PKU), hereditary spherocytosis, alpha-1-antitrypsin deficiency, Gaucher’s disease, achondroplastic dwarfism, hemophilia, or certain forms of diabetes (Figure 4.5). Point mutations may occur spontaneously because of occasional mistakes in the process of DNA replication, without any intervention of external factors. There are also agents in the environment including chemicals or radiation that promote or cause such mutations. These agents are called mutagens. When such mutations occur, they become part of all the daughter cells of that cell. If the mutations occur in the cells that lead to reproductive cells, these defective genes may be inherited just as are healthy genes.
Basic Molecular Cloning of DNA and RNA
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
Polymerases make mistakes, inserting the wrong base pair (a transition if it substitutes a purine for a purine or a pyrimidine for a pyrimidine, a transversion if it substitutes a purine for a pyrimidine or vice versa); failing to insert one or more base pairs (a deletion); or inserting one or more extra base pairs (an insertion). All of these are called mutations, and the mutation rate varies among polymerases: from about 4 × 10−7 errors per base pair per cycle for high-fidelity polymerases, to 2 × 10−5 per base pair per cycle for typical commercial Taq polymerase, to 5 × 10−3 per base pair per cycle for error-prone polymerase. Because of the degeneracy of the amino acid code, a single nucleotide error, called a point mutation, may not change the resulting protein; this is a silent mutation. If a different amino acid is substituted, it is called a missense mutation. These may change the protein’s function very little or tremendously, depending upon the location and the degree of change. The insertion of a stop codon leads to a truncated protein and is called a nonsense mutation (Figure 2.16). The insertion or deletion of 1 or 2 base pairs leads to a frameshift mutation, changing the encoding of all of the amino acids downstream of the error.
Conjugated Poly/Oligo-Electrolytes for Cancer Diagnosis and Therapy
Published in John R. Reynolds, Barry C. Thompson, Terje A. Skotheim, Conjugated Polymers, 2019
Lingyun Zhou, Guillermo C. Bazan, Shu Wang
More specific detection methods use fluorescent probe-labeled DNA and PCR techniques to examine single point mutations.80,83,84 The method is applicable to any SNP, as long as the nucleotide sequence is known and the mutation site is certain. The target genomic-template is amplified by PCR, followed by a separate single-base extension (SBE) reaction for each different allele using an allele-specific primer in the presence of a fluorescent molecule-labeled deoxynucleoside triphosphate (dNTP-Fl) or dideoxynucleotide triphosphate (ddNTP-Fl). There are two ways to design primer and to choose deoxynucleoside triphosphate (dNTP) or dideoxyribonucleotide triphosphate (ddNTP). 1: The primer 5’ ends exactly at the variant base in SNP DNA. The choice of dNTP-Fl/ddNTP-Fl should assure that the dNTP-Fl/ddNTP-Fl is complementary to the nucleotide immediately 5’ to the variant base in the SNP in the target DNA strand in order to incorporate dNTP-Fl to the 3’ end of extension primer. 2: The primer 5’ ends at one site before the variant base in SNP DNA. dNTP-Fl/ddNTP-Fl is complementary to the mutant nucleotide. Note that the target PCR products should be treated with shrimp alkaline phosphatase (SAP), exonuclease I, and pyrophosphatase to degrade redundant PCR primers, dNTPs, and pyrophosphate before carrying out the SBE reaction. The addition of CCP triggers FRET from CCP to the fluorescent tag only if the extension primers absolutely match the PCR products. By measuring changes in the fluorescence intensity of samples and the FRET ratio of emission intensities of conjugated polymer and labeling fluorescent molecule, SNP genotypes can be determined. In the second method, utilizing two different labelings of dNTP-Fls or ddNTP-Fls, which are complementary to wild type or mutant nucleotide, respectively, can acquire the percentage of mutant DNA in the tested DNA sample.
Improved bioethanol production using genome-shuffled Clostridium ragsdalei (DSM 15248) strains through syngas fermentation
Published in Biofuels, 2021
Siddhi Patankar, Amol Dudhane, A. D. Paradh, Sanjay Patil
Improvements in the performance of selected shuffled strains are seen mainly as a result of random mutagenesis and protoplast fusion. The process of mutagenesis introduces point mutation. During the process of genome shuffling, strains may acquire new characteristics as a result of recombination. Events such as deletion and duplication can also help in the acquisition of new traits [27]. The process of selection of promising fusants after protoplast fusion allows only those strains with stable mutation to be selected [39,40]. As these strains undergo recombination they produce a strain that has desirable traits. The strains obtained after several rounds of protoplast fusion and recursive mating are relatively stable and the chances of reversion in these strains are much reduced. The overall process results in highly promising strains in a short period of time [16].
Lemna minor, a hyperaccumulator shows elevated levels of Cd accumulation and genomic template stability in binary application of Cd and Ni: a physiological and genetic approach
Published in International Journal of Phytoremediation, 2021
Ibrahim Ilker Ozyigit, Lutfi Arda, Bestenur Yalcin, Ibrahim Ertugrul Yalcin, Bihter Ucar, Asli Hocaoglu-Ozyigit
Also, latter step of our work, Cd-Ni stress-induced genomic alterations in L. minor were determined through employing RAPD and ISSR markers. Several cellular stress responses occur due to heavy metal ions induction causing the appearances of damage on different plant cellular components including membranes, proteins and DNA (Sudmoon et al.2015). Existing DNA point mutations can be detected by employing PCR-based molecular markers (i.e. RAPD, AFLP and ISSR) that yield sensitive signals (Sorrentino et al.2017). Substantial alterations due to the formation of structural changes on DNA by various DNA mutations and lesions could influence PCR kinetics (Dogan et al.2012; Ozyigit, Yilmaz, et al.2016).
A dynamic optimization method for adaptive signal control in a connected vehicle environment
Published in Journal of Intelligent Transportation Systems, 2020
Zhihong Yao, Yangsheng Jiang, Bin Zhao, Xiaoling Luo, Bo Peng
Mutation can be divided into single-point mutation and multi-point mutation. To avoid the volatility of a solution that is too large to converge, the single-point mutation is applied as the mutation algorithm in this study. Similar to the crossover operation, the mutation operation first randomly selects one mutating point and then substitutes the original random number for another newly generated random number. For example, if the mutating point is at the second gene, then the chromosome will be after the mutation.