The remaining 23 free parameters were not fit to data, but were selected through a procedure that optimized the coherence of origin firing and minimized re-replication (selected as hypothetical goals of evolutionary 'design').
Induction of lytic replication selects for clones with increased K13 expression and NF-κB activity, while siRNA-mediated silencing of K13 induces the expression of lytic genes.
Thus, K13 confers survival advantage on KSHV-infected cells against lytic replication-induced cell death and, accordingly, induction of lytic replication selects for clones with increased K13 expression and NF-κB activity.
Twelve treatment groups with a total number of 768 experimental hatching eggs, four replications and 16 eggs in each replication were selected to form a completely randomized design of factorial arrangement.
Rep2, Rep5, Rep52aa146 (which divides region 1 and 2 of Rep and can replicate ITR2 and ITR5), and Rep25aa149 (essentially no ITR2 or ITR5 replication) were selected.
Colocalization and strong interaction are at the basis of the observed evolutionary (positive) feedback: Units of replication are selected (at least in the short run) if their close mutants replicate them more than the mutants themselves get replicated.
On each aspect a total of 36 random trees from different blocks (treatment replication) were selected (NNE = 36, NSW = 36, Ntotal = 72).
It remains to check if the tentative price, as given by the cost of replication or selected to be below the upper bound given by the minimal cost of superhedging, complies with some form of the no-arbitrage property of the extended market.
For replication we selected the individuals from KORA S4 survey (n = 1,830; BMI = 25.6±2.7 kg/m2; age = 52.7±9.0 years) that satisfied the same phenotype criteria as in GWAS with KORA S3.
To further analyze the role of the DDX3 insertion in the context of HIV-1 replication, we selected peptide ligands for the DDX3 insertion from phage displayed random peptide libraries.
