Sample shuffling

Brothman et al 24 have given an alternative theory for the process of mixing of solid particles, which has been described as a shuffling process. It is proposed that, as mixing takes place, there will be an increasing chance that a sample of a given size intercepts more than one part of the interface, and hence the number of mixed samples will increase... 

The positions of the amino acid substitutions identified in the various pNB esterases are illustrated in Fig. 7, on a model of the pNB esterase developed from the X-ray crystal structures of homologous enzymes [2]. Known beneficial mutations are indicated also shown are the mutations believed to be neutral or to affect expression. Positions of the additional translated mutations found in the variants produced by DNA shuffling are indicated by the white arrows. None of the effective amino acid substitutions lie in segments of the esterase predicted to interact directly with the bound substrate. It may be that the amino acid substitutions sampled at positions adjacent to the substrate were all... 

The limitations of DNA shuffling, arising from its dependency on sequence identity, have motivated the development of new technologies to facilitate an unbiased sampling of sequence space. At present, the reported approaches for creating sequence-independent hybrid libraries between two parental sequences include a family of methods collectively known as Incremental Truncation for the Creation of Hybrid enzYmes (ITCHY) [72,95,96] and Sequence-Homology Independent Protein RECom-bination (SHIPREC) [91]. 

Fig. 9.1 CDR shuffling into a master framework according the n-CoDeR concept. A primer set that was designed according to the master framework was used to amplify individual CDRs (that are numbered 1-3) with flanking framework sequences from the human cDNA libraries that were used as template (V I, VH2, and VH3 represent a sample of antibody genes that are present in the natural human repertoire that contains millions of such genes). The resulting PCR products contain CDRs with flanking framework sequences that overlap with each other, allowing assembly of intact...

Figure 13. Distributions of trapping times (1000 samples) calculated by left) a model that includes random shuffling of excitation energies in all the pigments except those of P700 and (right) random shuffling of excitation energies except those of the six RC pigments and the two linker Chls.

As an example, suppose a card is randomly dealt from a well-shuffled deck of 52 cards. The probability of this card being a heart is since there are 13 hearts in a deck. However, if you arc told that the dealt card is red, then the probability of a heart changes to because the sample space is reduced to just 26 cards. Likewise, if you are told that the dealt card is black, then P(Heart Black) = 0. 

For comparison with the sampled alignments, we evaluated the scores of shuffled globin sequences and non-globin sequences (including all alpha and other fold families). 

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