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Recombination among coexisting strains occurs at a rate approximately three times the mutation rate.
Theoretical and experimental studies have demonstrated that diversity of coexisting strains can arise in a population due to tradeoffs and variation in resistance phenotypes, and their costs are often associated with the efficiency of nutrient uptake [1], [13], [38].
In order to understand the ways in which virus-host interactions mediated by CRISPRs affect population dynamics, it is necessary to link signatures of resistance among coexisting strains to genotypic variation within a population.
Oscillations of different species' abundance are theorized to be damped by fitness trade-offs associated with the physiological costs of viral resistance, resulting in a stable level of diversity of coexisting strains within a population at any one time [10].
At the same time, some residual competition between all coexisting strains maintains a bounded pool of susceptible hosts and suppresses "speciations" of influenza A into independent lineages.
Coexisting strains have varying growth rates, but any selective benefit from increased growth rate is balanced by a cost from increased lysis, resulting in kill-the-winner dynamics [ 20, 21].
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Results from the model suggest that the strain fitness should be measured relative to the fitness landscape of coexisting recombinant strains.
The inference of clonal interference depends on both of these selection characteristics and imposes an additional constraint: in any model of the immune dynamics, compatibility with the genome data requires a rate of beneficial epitope mutations high enough to generate competition between coexisting mutant strains.
Sequencing of 20 plasmid clones from these PCR products again did not reveal minor strains coexisting along with the major strain.
During this period, the best cultures were freely shared between laboratories, and this coupled with the repeated isolation of individual strains with particular characteristics from commercial mixed strain starters, and the development of bacteriophage-insensitive cultures has resulted in many closely related strains coexisting.
Peña, A. et al. Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.
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