Mutations recombination and

Evolutionary computation which is learned by watching population dynamics the most important programming are genetic algorithms which are inspired by the evolutionary processes of mutation, recombination, and natural selection in biology. 

In this section, we explore the theoretical basis for each process in directed evolution mutation, recombination, and screening. Although this section is subdivided to discuss each process separately, the evolutionary parameters cannot be treated entirely independently. For example,... 

Many clues as to how to engineer better enzymes came from drawing parallel comparisons with nature and studying how nature has created authentic enzymes. By studying the evolution of bona fide proteins, it has been learned that they are hi ly adaptable, incessantly changing molecules. They can sometimes acclimatize to different environments and can even adopt unique functions, at least over evolutionary time scales. It is now known that the natural processes of mutation, recombination and se lection resulted in the creation of enzymes with varied functions through the evolution of a common ancestral protein of the same general structure (16),... 

Katz AJ, Chiu A, Beaubier J, Shi X. 2001. Combiniug Drosophila melanogaster somatic mutation-recombination and electron spin resonance spectroscopy data to interpret epidemiologic observations on chromium carcinogenicity. Mol Cell Biochem 222(l-2) 61-68. 

Vogel EW. 1985. The Drosphila somatic recombination and mutation assay (SRM) using the white-coral somatic eye color system. In Ashby J, de Serres FJ, et al., eds. Progress in mutation research. Vol. 5. Evaluation of short-term tests for carcinogens. Amsterdam, The Netherlands Elsevier Science Publishers, 313-317. 

After a number of new solutions are produced by crossover (or more generally, recombination) and mutation operations, improved solutions must be incorporated into the population. The best solution found thus far is almost always retained. A common strategy replaces a certain fraction of the remaining individuals, either with improved offspring or with new individuals chosen to maintain diversity. Another strategy is tournament selection, in which new solutions and current population members compete in a tournament. Each solution competes with K other solutions, which may be randomly selected, and, in each pairwise comparison, the solution with best fitness value wins. If P is the population size, the P solutions with the most wins become the new population. 

Mismatch Repair. Mispairs that break the normal base-pairing rules can arise spontaneously due to DNA biosynthetic errors, events associated with genetic recombination and the deamination of methylated cytosine (Modrich, 1987). With the latter, when cytosine deaminates to uracil, an endonuclease enzyme, /V-uracil-DNA glycosylase (Lindahl, 1979), excises the uracil residue before it can pair with adenine at the next replication. However, 5-methyl cytosine deaminates to form thymine and will not be excised by a glycosylase. As a result, thymine exits on one strand paired with guanine on the sister strand, that is, a mismatch. This will result in a spontaneous point mutation if left unrepaired. For this reason, methylated cytosines form spontaneous mutation hot-spots (Miller, 1985). The cell is able to repair mismatches by being able to distinguish between the DNA strand that exists before replication and a newly synthesized strand. 

Most DNA manipulations require the use of purified enzymes. Within cells these enzymes are used for DNA replication and transcription, breakdown of foreign DNA, repair of mutated DNA and recombination between different DNA molecules. Most of the purified enzymes are available commercially. They are usually supplied in Tris buffer containing 50% glycerol and are stored at -20 °C. The glycerol is included in the buffer to prevent freezing but must be removed prior to use as it alters the activity of some enzymes. 

All these techniques create genetic diversity by recombination and point mutations and are well developed. However, insertions and deletions (indels) are also important types of mutation which are probably underrepresented in many conventional mutagenesis strategies. Methods for incorporation of indels in predefined positions in a combinatorial manner have been developed.Although there are some published studies on their use in the directed evolution of biocatalysts,the full potential of these newer methods of gene mutation for enzyme improvement are yet to be demonstrated. 

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