Biomedical Engineering Reference
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Fig. 8.
The accumulated numbers of genes damaged because of the stop codon appearance in
their gene sequence from the leading and lagging strands for different mutational scenarios
of the changing pressure, clear fluctuations in the number of eliminated genes are vis-
ible during the simulation time. For every type of applied mutational pressure (direct,
reverse, and changing), the leading strand genes are always less frequently eliminated
than the lagging strand genes.
When the selection against stop codons is considered, the largest number of elimi-
nated genes are observed for genes located in the lagging strand and subjected to the
changing pressure whereas the elimination is the weakest for the leading strand genes
also under the changing pressure (Fig. 8). The numbers for simulations with constant
pressures take intermediate values between these two extremes. Considering the con-
stant mutational pressures, the accumulated numbers of eliminated genes are higher
when genes are under the pressure characteristic of the lagging strand. It is in the case
when the lagging pressure is reverse for the leading strand genes and direct for the lag-
ging genes. However, the excess is not well pronounced in this case and is visible after
2
.
5
million MCS. Till this time, the accumulated numbers of damaged lagging genes are
higher when they are under the leading strand pressure than the lagging strand pressure.
4
Discussion
In the paper, we have worked out a simulation model of bacterial genome evolution in
which the algorithm for finding protein coding signal and stop codon occurrence played
a role as selection criteria. In the simulations we used two mutational pressures asso-
ciated with DNA replication, which were applied to mutating of protein coding genes
from the leading and lagging DNA strands. The pressures were used as the constant
pressure through the whole simulation or they were applied alternately as the changing
pressure.
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