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Binary Linear Congruence Code
Published in Khodakhast Bibak, Restricted Congruences in Computing, 2020
Deletions or insertions can occur in many systems; for example, they can occur in some communication and storage channels and in biological sequences. A deletion or insertion in a DNA sequence leads to a genetic mutation known as the frameshift mutation. Therefore, studying deletion/insertion correcting codes may lead to important insight into genetic processes and into many communication problems. Deletion correcting codes have been the subject of intense research for more than fifty years [139; 144; 181], with recent results settling long-standing open problems regarding constructions of multiple deletion correcting codes with low redundancy [34; 37]. Nevertheless, our understanding about these codes and channels with this type of error is still very limited, and many open problems in the area remain, especially when considering constructions of deletion correcting codes that satisfy additional constraints, such as weight or parity constraints. Examples include codes in the Damerau distance [67], based on single deletion correcting codes with even weight, and Shifted Varshamov–Tenengolts codes [172] used for burst deletion correction. In such settings, one important question is to determine the weight enumerators of the component deletion correcting codes in order to estimate the size [47; 111] of the weight-constrained deletion correcting codes. The component deletion correcting code is frequently defined in terms of a linear congruence for which the number of solutions of some fixed weight determines the size of the constrained code.
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.
Pistacia lentiscus L. fruits showed promising antimutagenic and antigenotoxic activity using both in-vitro and in-vivo test systems
Published in Journal of Toxicology and Environmental Health, Part A, 2022
Ghania Bouguellid, Nadjet Debbache-Benaida, Dina Atmani-Kilani, Chiara Russo, Margherita Lavorgna, Concetta Piscitelli, Karima Ayouni, Meriem Berboucha-Rahmani, Marina Isidori, Djebbar Atmani
Mutagenicity was tested using the Salmonella/microsome assay with and without metabolic activation based upon the plate incorporation method (D’Abrosca et al. 2017; Maron and Ames 1983; Mortelmans and Zeiger 2000) against two tester strains (TA98 and TA100) as they detect the vast majority of mutagens. TA98 strain was used to measure frameshift mutations, while TA100 was used to assess base-pair substitutions (Verschaeve and Van Staden 2008).